tag:blogger.com,1999:blog-4004457723427864302024-02-20T16:18:53.844-08:00The Fungi Phylogenetic ProjectSALSA HPChttp://www.blogger.com/profile/02024051316999832941noreply@blogger.comBlogger30125tag:blogger.com,1999:blog-400445772342786430.post-61514647738796891522014-06-04T10:53:00.001-07:002014-06-04T10:54:41.054-07:00GSF D1/D2 Data: Statistics<br />
<ul>
<li>Original Sequence Counts</li>
<ul>
<li>D1 - 265655</li>
<li>Reversed D2 - 265655</li>
</ul>
<li>Paired Unique Sequence Counts</li>
<ul>
<li>D1 - 143223</li>
<li>Reversed D2 - 143223</li>
</ul>
<li>Average Lengths</li>
<ul>
<li>Paired Unique D1 - 254</li>
<li>Paired Unique Reversed D2 - 247</li>
</ul>
</ul>
<div>
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<div>
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<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<ul>
<li>Paired Unique D1 Sequence Length Histogram</li>
</ul>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhgHTJ0okgdyyHnsXTF_VUvVMb0F2vQcQIa9hax9sAJf3gxK2rtVX9_6DqZpGW__RevL9jtM9AINF_PRigCaGH-DVZ41f0-EHC2-Qboltsvd300BRizj8blZBWnIQrEujE3C5KuHnXaPoE/s1600/plot_paired_unique_143223_All_AMF_Retained_Paired_Read1_D1_Region_index.txt_histogram.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhgHTJ0okgdyyHnsXTF_VUvVMb0F2vQcQIa9hax9sAJf3gxK2rtVX9_6DqZpGW__RevL9jtM9AINF_PRigCaGH-DVZ41f0-EHC2-Qboltsvd300BRizj8blZBWnIQrEujE3C5KuHnXaPoE/s1600/plot_paired_unique_143223_All_AMF_Retained_Paired_Read1_D1_Region_index.txt_histogram.png" height="640" width="640" /></a><br /><div class="separator" style="clear: both; text-align: center;">
<br /></div>
<ul>
<li>Paired Unique Reversed D2 Sequence Length Histogram</li>
</ul>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhkmqzHBFcF3kYAtnFT8enaXx0ZAMITx9fA6G33OsPcPFWn5yoPffNH0WJH57M-ML7D00TDMiZOKK_iVb5GiaKmiw4Qg5LhZxS8BZgVNECHGwWcqOAaB8TN_V8t0l3Ne3jJg7-fZCTGSsM/s1600/plot_paired_unique_143223_All_AMF_Retained_Paired_Read2_ReverseCompl_D2_Region_index.txt_histogram.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhkmqzHBFcF3kYAtnFT8enaXx0ZAMITx9fA6G33OsPcPFWn5yoPffNH0WJH57M-ML7D00TDMiZOKK_iVb5GiaKmiw4Qg5LhZxS8BZgVNECHGwWcqOAaB8TN_V8t0l3Ne3jJg7-fZCTGSsM/s1600/plot_paired_unique_143223_All_AMF_Retained_Paired_Read2_ReverseCompl_D2_Region_index.txt_histogram.png" height="640" width="640" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
</div>
<div>
<br /></div>
Saliya Ekanayakehttp://www.blogger.com/profile/10281589417412608237noreply@blogger.com0tag:blogger.com,1999:blog-400445772342786430.post-57213989681648534342014-04-27T12:40:00.000-07:002014-06-04T08:44:25.935-07:00GSF R1/R2 Data: R2 Statistics<br />
<div class="separator" style="clear: both; text-align: left;">
The following figures present statistics for a selected 100k of R2 dataset along with the so called "Master" data set of 1020 sequences. </div>
<div class="separator" style="clear: both; text-align: left;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
Summary of Content</div>
<div class="separator" style="clear: both; text-align: left;">
</div>
<ul>
<li>Histograms</li>
<ul>
<li>SWG Alignment length of R2 with itself (top left)</li>
<li>SWG Alignment length of Reversed R2 with Master (top right)</li>
<li>SWG PID of R2 with itself (bottom left)</li>
<li>SWG PID of Reversed R2 with Master (bottom right)</li>
</ul>
<li>Heatmaps for SWG PID of R2 with itself against alignment length. Also with alignment length cut</li>
<li>Heatmap for SWG PID of Reversed R2 with Master against alignment length.</li>
<li>Heatmap for SWG alignment length of Reversed R2 with Master against Non-reversed R2 with Master</li>
<li>Heatmap for SWG score of Reversed R2 with Master against Non-reversed R2 with Master</li>
<ul>
</ul>
</ul>
<br />
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<ul>
<li><b>Histograms</b></li>
</ul>
<b><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjgxU2_rEjy8QitXXiSlohiYZ84pNqnYMi74kvoxOaBK9oJRHB6qlFUycAhjsmKfUNmbWJpFtqHTXFpGb4VR1LJSqb8u1kE3T6lvMJBzwodOn96QtTVgq2Vh2QxQNzIVUi_oSTgbM45aKE/s1600/r2_histograms.png" imageanchor="1" style="font-weight: normal; margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjgxU2_rEjy8QitXXiSlohiYZ84pNqnYMi74kvoxOaBK9oJRHB6qlFUycAhjsmKfUNmbWJpFtqHTXFpGb4VR1LJSqb8u1kE3T6lvMJBzwodOn96QtTVgq2Vh2QxQNzIVUi_oSTgbM45aKE/s1600/r2_histograms.png" height="640" width="640" /></a></b><br />
<ul>
<li style="border: none; color: #333333; margin: 0px 0px 0.25em; padding: 0.25em 0px;"><b>R2 SWG PID Vs R2 SWG Align Length -- length cut > 100 on right</b></li>
</ul>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgugsxUOx0fgXncna6L04gGPdZEBZla-gQD-2sa_H2qewEcWvqVM4aXTUe4roXz9ImF6B1pmbH5tNJQrr25FqfjDp6iaFceBRyZR90yMgyXDuaAcV1o0Afs7DFr7BBusH6Dv5h5NzvJMvI/s1600/whole-plot-gsf-100k-R2-swg-pid-Vs-gsf-100k-R2-swg-alignlenDensitySat%5B0.85%5D-large.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgugsxUOx0fgXncna6L04gGPdZEBZla-gQD-2sa_H2qewEcWvqVM4aXTUe4roXz9ImF6B1pmbH5tNJQrr25FqfjDp6iaFceBRyZR90yMgyXDuaAcV1o0Afs7DFr7BBusH6Dv5h5NzvJMvI/s1600/whole-plot-gsf-100k-R2-swg-pid-Vs-gsf-100k-R2-swg-alignlenDensitySat%5B0.85%5D-large.png" height="450" width="450" /></a><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhCY6_dqWa-ylpFhf5Oz5IV27bDrbBInHHPTCErESbSjoBVEXZtJGHhcsUppxZiJ_ZJD8UaJxrn_JEOhEBs8001TDNENc7uS0XTcI0qvFNt-X3T0ERX8qKX1pBji-43TM6mlY6YAh92df0/s1600/whole-plot-gsf-100k-R2-swg-pid-Vs-gsf-100k-R2-swg-alignlenDensitySat%5B0.85%5D-large.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhCY6_dqWa-ylpFhf5Oz5IV27bDrbBInHHPTCErESbSjoBVEXZtJGHhcsUppxZiJ_ZJD8UaJxrn_JEOhEBs8001TDNENc7uS0XTcI0qvFNt-X3T0ERX8qKX1pBji-43TM6mlY6YAh92df0/s1600/whole-plot-gsf-100k-R2-swg-pid-Vs-gsf-100k-R2-swg-alignlenDensitySat%5B0.85%5D-large.png" height="450" width="450" /></a>
<br />
<ul>
<li><b>Reversed R2 100K + Master 1020 SWG PID Vs. Alignment Length</b></li>
</ul>
<b><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgx3Lf-8sdbBTxWlZW_Tyy2oNYP1gxiZz6u49oPTGgXSy91gM6HdOJTUtu45cXcZZef1wjMwWQz7REDcpW9OSE682F5mVxtwLCaJ-kOgwojSNgQk8gb9WrRPvMj95F4NerAAiAFGsDzhoY/s1600/whole-plot-100k_1020_RevR2_swg_pid-Vs-100k_1020_RevR2_alignlenDensitySat%5B0.85%5D-large.png" imageanchor="1" style="font-weight: normal; margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgx3Lf-8sdbBTxWlZW_Tyy2oNYP1gxiZz6u49oPTGgXSy91gM6HdOJTUtu45cXcZZef1wjMwWQz7REDcpW9OSE682F5mVxtwLCaJ-kOgwojSNgQk8gb9WrRPvMj95F4NerAAiAFGsDzhoY/s1600/whole-plot-100k_1020_RevR2_swg_pid-Vs-100k_1020_RevR2_alignlenDensitySat%5B0.85%5D-large.png" height="640" width="640" /></a></b>
<br />
<ul>
<li><b>100K+1020 R2 Reversed Alignment Length Vs Alignment Length</b></li>
</ul>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiOfL8eszICaTbLLr1nyEA_k2kQgrtCg4g1OIsfLt11nJEbyUy-e8zVqFAOTbv5wwf2ycgNyH6chpdNgTswBQYO9wEIKGU9h4LavDgP0f5S18vDtqjKpDMwkJk3yxarPmZ3_Vsmgyx7aSE/s1600/whole-plot-100k_1020_rev_alignlen-Vs-100k_1020_alignlenDensitySat%5B0.85%5D-large.png" imageanchor="1" style="font-weight: normal; margin-left: 1em; margin-right: 1em; text-align: center;">
<img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiOfL8eszICaTbLLr1nyEA_k2kQgrtCg4g1OIsfLt11nJEbyUy-e8zVqFAOTbv5wwf2ycgNyH6chpdNgTswBQYO9wEIKGU9h4LavDgP0f5S18vDtqjKpDMwkJk3yxarPmZ3_Vsmgyx7aSE/s1600/whole-plot-100k_1020_rev_alignlen-Vs-100k_1020_alignlenDensitySat%5B0.85%5D-large.png" height="640" width="640" /></a><br />
<ul>
<li><b>100K+1020 R2 Reversed Score Vs Score</b></li>
</ul>
<b>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgMeHqTaGV5jFt_A2_MRTuel59ewHJzIa-RCmVAkQTtm99DXfK_nGg9Kb5mhuM1lqa7XtBo_1PUNYhJCbLSu4Ov32NdCeS0YUQMRv9dc5ek6HqUdCRaPETFcSzrs8EipE2rH3y7fvfbLRY/s1600/whole-plot-100k_1020_rev_score-Vs-100k_1020_scoreDensitySat%5B0.85%5D-large.png" imageanchor="1" style="font-weight: normal; margin-left: 1em; margin-right: 1em; text-align: center;">
<img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgMeHqTaGV5jFt_A2_MRTuel59ewHJzIa-RCmVAkQTtm99DXfK_nGg9Kb5mhuM1lqa7XtBo_1PUNYhJCbLSu4Ov32NdCeS0YUQMRv9dc5ek6HqUdCRaPETFcSzrs8EipE2rH3y7fvfbLRY/s1600/whole-plot-100k_1020_rev_score-Vs-100k_1020_scoreDensitySat%5B0.85%5D-large.png" height="640" width="640" />
</a>
</b>Saliya Ekanayakehttp://www.blogger.com/profile/10281589417412608237noreply@blogger.com0tag:blogger.com,1999:blog-400445772342786430.post-56903946572113865252014-04-27T09:57:00.000-07:002014-06-04T08:44:15.132-07:00GSF R1/R2 Data: Heatmaps for (R1/R2) + "Master" Data - 2<br />
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<ul>
<li><b>R1 100K + Master 1020 SWG PID Vs. Alignment Length</b></li>
</ul>
<b><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_jF57bdaVXk8rjJ22nEbtxpgCx6toGmnOel2cTEypUznQKM7GIYNatIBrXG5Aq0y5jyEEfXVjw9_UhuMy2XncTg3-JrGmkqdUyxDxzYYQBJE5pTdUDzV_pb8BsUCvYDnqlDkTiMxb7dM/s1600/whole-plot-100k_1020_R1_swg_pid-Vs-100k_1020_R1_alignlenDensitySat%5B0.85%5D-large.png" imageanchor="1" style="font-weight: normal; margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh_jF57bdaVXk8rjJ22nEbtxpgCx6toGmnOel2cTEypUznQKM7GIYNatIBrXG5Aq0y5jyEEfXVjw9_UhuMy2XncTg3-JrGmkqdUyxDxzYYQBJE5pTdUDzV_pb8BsUCvYDnqlDkTiMxb7dM/s1600/whole-plot-100k_1020_R1_swg_pid-Vs-100k_1020_R1_alignlenDensitySat%5B0.85%5D-large.png" height="640" width="640" /></a></b><br />
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<ul>
<li><b>Reversed R2 100K + Master 1020 SWG PID Vs. Alignment Length</b></li>
</ul>
<b><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgx3Lf-8sdbBTxWlZW_Tyy2oNYP1gxiZz6u49oPTGgXSy91gM6HdOJTUtu45cXcZZef1wjMwWQz7REDcpW9OSE682F5mVxtwLCaJ-kOgwojSNgQk8gb9WrRPvMj95F4NerAAiAFGsDzhoY/s1600/whole-plot-100k_1020_RevR2_swg_pid-Vs-100k_1020_RevR2_alignlenDensitySat%5B0.85%5D-large.png" imageanchor="1" style="font-weight: normal; margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgx3Lf-8sdbBTxWlZW_Tyy2oNYP1gxiZz6u49oPTGgXSy91gM6HdOJTUtu45cXcZZef1wjMwWQz7REDcpW9OSE682F5mVxtwLCaJ-kOgwojSNgQk8gb9WrRPvMj95F4NerAAiAFGsDzhoY/s1600/whole-plot-100k_1020_RevR2_swg_pid-Vs-100k_1020_RevR2_alignlenDensitySat%5B0.85%5D-large.png" height="640" width="640" /></a></b>Saliya Ekanayakehttp://www.blogger.com/profile/10281589417412608237noreply@blogger.com0tag:blogger.com,1999:blog-400445772342786430.post-49039059379573535552014-04-22T12:21:00.001-07:002014-06-04T08:43:53.577-07:00GSF R1/R2 Data: Histograms for (R1/R2) + "Master" Data<div class="separator" style="clear: both; text-align: center;">
</div>
<div>
<br />
<ul>
<li><b>SWG Alignment Lengths</b></li>
</ul>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgSRbdH341z7T1NqzfT8BVlJWMHWovMi5LykC9ijC489Wy7Coa-R492BSU2ouLlbBsPU7ohA9EBDOKRBxn4siDO1M-9NYtC-xTA7sEpy0DGoJW8U7cJ6G4xekoBe4U9qK_UeUBneMC29T8/s1600/alignment_length_histogram.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgSRbdH341z7T1NqzfT8BVlJWMHWovMi5LykC9ijC489Wy7Coa-R492BSU2ouLlbBsPU7ohA9EBDOKRBxn4siDO1M-9NYtC-xTA7sEpy0DGoJW8U7cJ6G4xekoBe4U9qK_UeUBneMC29T8/s1600/alignment_length_histogram.png" height="640" width="640" /></a>
<br />
<br />
<ul>
<li><b>SWG PID</b></li>
</ul>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgO9P9X46cntZSzb5G9je-24zGRVIOmA2mc5OkfyyZmQYdZectHcZOWJn2ijZhWgCvtUGNeqKoIQr9ztjicVAzyXKTBucjY3MFNmz_kxkN32cxQVhmF-chPpEr7fdNDq1vsBGwdvrqNESA/s1600/swg_pid_histogram.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgO9P9X46cntZSzb5G9je-24zGRVIOmA2mc5OkfyyZmQYdZectHcZOWJn2ijZhWgCvtUGNeqKoIQr9ztjicVAzyXKTBucjY3MFNmz_kxkN32cxQVhmF-chPpEr7fdNDq1vsBGwdvrqNESA/s1600/swg_pid_histogram.png" height="640" width="640" /></a></div>
Saliya Ekanayakehttp://www.blogger.com/profile/10281589417412608237noreply@blogger.com0tag:blogger.com,1999:blog-400445772342786430.post-78109789638509097642014-04-19T21:15:00.000-07:002014-06-04T08:43:07.842-07:00GSF R1/R2 Data: Heatmaps for (R1/R2) + "Master" Data<ul>
<li><b>100K+1020 R1 Reversed Alignment Length Vs Alignment Length</b></li>
</ul>
<b>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiNMhLrlYbSM7QBEuS5QsDodTUZt0-41ZtdcqQYlMxiKRzOzu9m0tJPPcB54XP70QQr6O8eOphhlAZnOlVdnAgZVEXDN1WhoAzTPO8w0-2tNvtfH_gBwMARRyzrHVBR3KX14_MlefjXTU8/s1600/whole-plot-100k_1020_R1_rev_alignlen-Vs-100k_1020_R1_alignlenDensitySat%5B0.85%5D-large.png" imageanchor="1" style="font-weight: normal; margin-left: 1em; margin-right: 1em; text-align: center;">
<img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiNMhLrlYbSM7QBEuS5QsDodTUZt0-41ZtdcqQYlMxiKRzOzu9m0tJPPcB54XP70QQr6O8eOphhlAZnOlVdnAgZVEXDN1WhoAzTPO8w0-2tNvtfH_gBwMARRyzrHVBR3KX14_MlefjXTU8/s1600/whole-plot-100k_1020_R1_rev_alignlen-Vs-100k_1020_R1_alignlenDensitySat%5B0.85%5D-large.png" height="640" width="640" />
</a>
</b>
<br />
<ul>
<li><b>100K+1020 R1 Reversed Score Vs Score</b></li>
</ul>
<b>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjVwwFpxToLqaKz31TUJeQVbWxz93dlk4077iH3TainAZFUzBKAgr-iwpetkWxEV2px3_gtgNiRjVCYr04JK0N18668Tt9LLFVYWtxoygZirwZJl-2RDqsKkpTN5jshCcP6v6lAWaUqM_s/s1600/whole-plot-100k_1020_R1_rev_score-Vs-100k_1020_R1_scoreDensitySat%5B0.85%5D-large.png" imageanchor="1" style="font-weight: normal; margin-left: 1em; margin-right: 1em; text-align: center;">
<img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjVwwFpxToLqaKz31TUJeQVbWxz93dlk4077iH3TainAZFUzBKAgr-iwpetkWxEV2px3_gtgNiRjVCYr04JK0N18668Tt9LLFVYWtxoygZirwZJl-2RDqsKkpTN5jshCcP6v6lAWaUqM_s/s1600/whole-plot-100k_1020_R1_rev_score-Vs-100k_1020_R1_scoreDensitySat%5B0.85%5D-large.png" height="640" width="640" />
</a>
</b>
<br />
<ul>
<li><b>100K+1020 R2 Reversed Alignment Length Vs Alignment Length</b></li>
</ul>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiOfL8eszICaTbLLr1nyEA_k2kQgrtCg4g1OIsfLt11nJEbyUy-e8zVqFAOTbv5wwf2ycgNyH6chpdNgTswBQYO9wEIKGU9h4LavDgP0f5S18vDtqjKpDMwkJk3yxarPmZ3_Vsmgyx7aSE/s1600/whole-plot-100k_1020_rev_alignlen-Vs-100k_1020_alignlenDensitySat%5B0.85%5D-large.png" imageanchor="1" style="font-weight: normal; margin-left: 1em; margin-right: 1em; text-align: center;">
<img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiOfL8eszICaTbLLr1nyEA_k2kQgrtCg4g1OIsfLt11nJEbyUy-e8zVqFAOTbv5wwf2ycgNyH6chpdNgTswBQYO9wEIKGU9h4LavDgP0f5S18vDtqjKpDMwkJk3yxarPmZ3_Vsmgyx7aSE/s1600/whole-plot-100k_1020_rev_alignlen-Vs-100k_1020_alignlenDensitySat%5B0.85%5D-large.png" height="640" width="640" /></a><br />
<ul>
<li><b>100K+1020 R2 Reversed Score Vs Score</b></li>
</ul>
<b>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgMeHqTaGV5jFt_A2_MRTuel59ewHJzIa-RCmVAkQTtm99DXfK_nGg9Kb5mhuM1lqa7XtBo_1PUNYhJCbLSu4Ov32NdCeS0YUQMRv9dc5ek6HqUdCRaPETFcSzrs8EipE2rH3y7fvfbLRY/s1600/whole-plot-100k_1020_rev_score-Vs-100k_1020_scoreDensitySat%5B0.85%5D-large.png" imageanchor="1" style="font-weight: normal; margin-left: 1em; margin-right: 1em; text-align: center;">
<img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgMeHqTaGV5jFt_A2_MRTuel59ewHJzIa-RCmVAkQTtm99DXfK_nGg9Kb5mhuM1lqa7XtBo_1PUNYhJCbLSu4Ov32NdCeS0YUQMRv9dc5ek6HqUdCRaPETFcSzrs8EipE2rH3y7fvfbLRY/s1600/whole-plot-100k_1020_rev_score-Vs-100k_1020_scoreDensitySat%5B0.85%5D-large.png" height="640" width="640" />
</a>
</b>Saliya Ekanayakehttp://www.blogger.com/profile/10281589417412608237noreply@blogger.com0tag:blogger.com,1999:blog-400445772342786430.post-67793663019000396842014-04-15T13:00:00.000-07:002014-06-04T08:43:24.814-07:00GSF R1/R2 Data: Heatmaps for (R1/R2) DataHeatmaps for corresponding 100k random samples of GSF data.<br />
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<ul>
<li><b>R2 SWG PID Vs R1 SWG PID</b></li>
</ul>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiipZ8tlOhtCsb088AKLWAZSItwdo3Jo5M00cFwPSrXLayfaYPzuARyRiC_rZhj0flYeIvjYzbSVSWK7p9zWTjkJoe8QFbgXp5VnFBaThVnQ047oLDHVtaxfYixClE8vFVj2NshZP-cpJQ/s1600/whole-plot-gsf-100k-R2-swg-pid-Vs-gsf-100k-R1-swg-pidDensitySat%5B0.85%5D-large.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiipZ8tlOhtCsb088AKLWAZSItwdo3Jo5M00cFwPSrXLayfaYPzuARyRiC_rZhj0flYeIvjYzbSVSWK7p9zWTjkJoe8QFbgXp5VnFBaThVnQ047oLDHVtaxfYixClE8vFVj2NshZP-cpJQ/s1600/whole-plot-gsf-100k-R2-swg-pid-Vs-gsf-100k-R1-swg-pidDensitySat%5B0.85%5D-large.png" height="640" width="640" /></a><br />
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<ul>
<li><b>R1 SWG PID Vs R1 SWG Align Length -- length cut > 100 on right</b></li>
</ul>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhdQR64hyphenhyphenbP-K1zfGgiAWqXtN1sf0vCLAZzBCKhcUb4NoPd-Gmzahaqu8NSFzEDw6BAfO2f-NyiDybbz7CEqkbAr2LWTcxtbyKsD8RPpUNN5mNyvOOvBGmQdA8JIk2PP7Bmb2gOMBEusyk/s1600/whole-plot-gsf-100k-R1-swg-pid-Vs-gsf-100k-R1-swg-alignlenDensitySat%5B0.85%5D-large.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhdQR64hyphenhyphenbP-K1zfGgiAWqXtN1sf0vCLAZzBCKhcUb4NoPd-Gmzahaqu8NSFzEDw6BAfO2f-NyiDybbz7CEqkbAr2LWTcxtbyKsD8RPpUNN5mNyvOOvBGmQdA8JIk2PP7Bmb2gOMBEusyk/s1600/whole-plot-gsf-100k-R1-swg-pid-Vs-gsf-100k-R1-swg-alignlenDensitySat%5B0.85%5D-large.png" height="450" width="450" /></a><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh09TLZBCNBv2e_0fRb4ZdIu_LIP-tIZhhI_K9vksxNd1bhNdNOo17XKBhvBcJG4iHC_1NVxJz8nNJH17FYsXCWIph_lU2t-ey6hEw0VL5WVXFwomXvdbnXKeTTssfgAlhG_m7Dbb1Lm8Q/s1600/whole-plot-gsf-100k-R1-swg-pid-Vs-gsf-100k-R1-swg-alignlenDensitySat%5B0.85%5D-large.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh09TLZBCNBv2e_0fRb4ZdIu_LIP-tIZhhI_K9vksxNd1bhNdNOo17XKBhvBcJG4iHC_1NVxJz8nNJH17FYsXCWIph_lU2t-ey6hEw0VL5WVXFwomXvdbnXKeTTssfgAlhG_m7Dbb1Lm8Q/s1600/whole-plot-gsf-100k-R1-swg-pid-Vs-gsf-100k-R1-swg-alignlenDensitySat%5B0.85%5D-large.png" height="450" width="450" /></a><br />
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<ul>
<li><b>R2 SWG PID Vs R2 SWG Align Length -- length cut > 100 on right</b></li>
</ul>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgugsxUOx0fgXncna6L04gGPdZEBZla-gQD-2sa_H2qewEcWvqVM4aXTUe4roXz9ImF6B1pmbH5tNJQrr25FqfjDp6iaFceBRyZR90yMgyXDuaAcV1o0Afs7DFr7BBusH6Dv5h5NzvJMvI/s1600/whole-plot-gsf-100k-R2-swg-pid-Vs-gsf-100k-R2-swg-alignlenDensitySat%5B0.85%5D-large.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgugsxUOx0fgXncna6L04gGPdZEBZla-gQD-2sa_H2qewEcWvqVM4aXTUe4roXz9ImF6B1pmbH5tNJQrr25FqfjDp6iaFceBRyZR90yMgyXDuaAcV1o0Afs7DFr7BBusH6Dv5h5NzvJMvI/s1600/whole-plot-gsf-100k-R2-swg-pid-Vs-gsf-100k-R2-swg-alignlenDensitySat%5B0.85%5D-large.png" height="450" width="450" /></a><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhCY6_dqWa-ylpFhf5Oz5IV27bDrbBInHHPTCErESbSjoBVEXZtJGHhcsUppxZiJ_ZJD8UaJxrn_JEOhEBs8001TDNENc7uS0XTcI0qvFNt-X3T0ERX8qKX1pBji-43TM6mlY6YAh92df0/s1600/whole-plot-gsf-100k-R2-swg-pid-Vs-gsf-100k-R2-swg-alignlenDensitySat%5B0.85%5D-large.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhCY6_dqWa-ylpFhf5Oz5IV27bDrbBInHHPTCErESbSjoBVEXZtJGHhcsUppxZiJ_ZJD8UaJxrn_JEOhEBs8001TDNENc7uS0XTcI0qvFNt-X3T0ERX8qKX1pBji-43TM6mlY6YAh92df0/s1600/whole-plot-gsf-100k-R2-swg-pid-Vs-gsf-100k-R2-swg-alignlenDensitySat%5B0.85%5D-large.png" height="450" width="450" /></a>Saliya Ekanayakehttp://www.blogger.com/profile/10281589417412608237noreply@blogger.com0tag:blogger.com,1999:blog-400445772342786430.post-51396980713082971802013-10-11T09:43:00.000-07:002014-03-19T17:15:28.769-07:00revised 599nts and 999nts Raxml vs Clustering using Spherical Phylogenetic Tree<br />
<h3>
<span style="font-size: large;">Dataset</span></h3>
1. revised 599nts<br />
This work follows the previous work on <a href="http://salsafungiphy.blogspot.com/2013/09/pairwise-distances-from-msa-vs-pairwise.html">http://salsafungiphy.blogspot.com/2013/09/pairwise-distances-from-msa-vs-pairwise.html</a><br />
This dataset has a total number of 831 sequences.<br />
2. 999nts<br />
This work follows the previous work on <a href="http://salsafungiphy.blogspot.com/2013/06/pairwise-distances-from-multiple.html">http://salsafungiphy.blogspot.com/2013/06/pairwise-distances-from-multiple.html</a><br />
This dataset has a total number of 1306 sequences.<br />
<br />
<h3>
<span style="font-size: large;">Alignment</span></h3>
The clustering was done based on<br />
1) SWG, using EDNAFULL scoring matrix, with gap open = -16 and gap extension = -4<br />
2) Multiple sequence alignment, PID.<br />
<br />
The Raxml was done based on multiple sequence alignment,<br />
1) revised 599nts, <a href="https://iu.box.com/s/upsibig19dct8ulbrjz7">newick file</a><br />
2) 999nts, <a href="https://iu.box.com/s/9xf1qjvmlp6hsgc78nx5">newwick file</a><br />
<br />
<h3>
<span style="font-size: large;">Spherical Tree</span></h3>
The information of spherical tree can be found on previous work of <a href="http://salsafungiphy.blogspot.com/2012/11/phylogenetic-tree-generation-for.html">http://salsafungiphy.blogspot.com/2012/11/phylogenetic-tree-generation-for.html</a> and <a href="http://salsafungiphy.blogspot.com/2012/11/phylogenetic-tree-mega-table.html">http://salsafungiphy.blogspot.com/2012/11/phylogenetic-tree-mega-table.html</a><br />
<h4>
<b>Dimension Reduction</b></h4>
<b>Manxcat SMACOF:</b><br />
The pviz file for SWG clustering result with revised 599nts is <a href="https://iu.box.com/s/dyz522k97zyzibqe2874">here</a>, for 999nts is <a href="https://iu.box.com/s/bqjwo99x5gsabv86ylyi">here</a>.<br />
For MSA clustering result with revised 599nts is <a href="https://iu.box.com/s/syx63qqncgxnn7nv2zuz">here</a>, for 999nts is <a href="https://iu.box.com/s/tqh6bcfsmyzuvz2q9dbj">here</a>.<br />
<b>WDA-SMACOF:</b><br />
alpha set to 0.95<br />
The pviz file for SWG clustering result with revised 599nts is <a href="https://iu.box.com/s/aa5bnqw9dg9yuna4vy2i">here</a>, for 999nts is <a href="https://iu.box.com/s/98gqpqx774p1ipqwl802">here</a>.<br />
For MSA clustering result with revised 599nts is <a href="https://iu.box.com/s/4p6tkq7r9xc3r2gfq9nu">here</a>, for 999nts is <a href="https://iu.box.com/s/fmz8auvw8dflkj39tg52">here</a>.<br />
<h4>
Sum of branch lengths (edge sum)</h4>
<div>
(note that the difference of edge sum between SWG and MSA should due to the difference of the original distances of the clustering plot)</div>
<table border="1"><tbody>
<tr><td></td><td colspan="2">Manxcat SMACOF</td><td colspan="2">WDA-SMACOF</td>
</tr>
<tr><td></td><td>revised 599nts</td><td>999nts</td><td>revised 599nts</td><td>999nts</td></tr>
<tr><td>SWG</td><td>19.37</td><td>19.89</td><td>16.01</td><td>12.74</td></tr>
<tr><td>MSA</td><td>16.62</td><td>16.36</td><td>15.20</td><td>13.65</td></tr>
</tbody></table>
1) revised 599nts spherical tree<br />
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<tr><td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiV8MlkXhRirebO7xDKPxvR-c6d73iel9D0CtEePjWSLFFduChEAkWCxM5hpstZ9ApI0x9I7oaa3CvHIPaYLYTvkNyZuN8R8zrkCUa-g3dQm9Xdy7MCG1nZvsiWMR7W6Jmiv2vWUNX-RaNX/s1600/AMF_Phylo_revised_599nts_MSAPID_smacof_points_nj.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiV8MlkXhRirebO7xDKPxvR-c6d73iel9D0CtEePjWSLFFduChEAkWCxM5hpstZ9ApI0x9I7oaa3CvHIPaYLYTvkNyZuN8R8zrkCUa-g3dQm9Xdy7MCG1nZvsiWMR7W6Jmiv2vWUNX-RaNX/s1600/AMF_Phylo_revised_599nts_MSAPID_smacof_points_nj.png" height="207" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="font-size: 13px;">MSA Result</td></tr>
</tbody></table>
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj0QADy-ZGkAPLhZgtmnM80vBuS49m8-VmA_4u4vTQYdjL-ZZAbAi95rdu8krh-o1glX557q7V-bmOiFrxvx3H2uubKGQNDAR3yTTYo4BEbl1XNlikmOO2AMsYWz-eP04coN_4VcvEKESbM/s1600/AMF_Phylo_revised_599nts_SWGPID_smacof_points_nj.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj0QADy-ZGkAPLhZgtmnM80vBuS49m8-VmA_4u4vTQYdjL-ZZAbAi95rdu8krh-o1glX557q7V-bmOiFrxvx3H2uubKGQNDAR3yTTYo4BEbl1XNlikmOO2AMsYWz-eP04coN_4VcvEKESbM/s1600/AMF_Phylo_revised_599nts_SWGPID_smacof_points_nj.png" height="207" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="font-size: 13px;">SWG Result</td></tr>
</tbody></table>
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2) 999nts spherical tree<br />
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<tr><td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhk6MbmJNW1fov0BTOxU52BsnN-RnRQPY2x8cyb84fHCHAjwa3FWAyvL6IzLvMMcuOibAshiLaO6RYVyT7IklfNvpzyy1RbnjoJzdm4D84ee5yj6l-2hn-DcBRKnjyvnCzcjdq_OLKzJvc1/s1600/AMF_Phylo_Seqs_999Nts_Apr17MAFFT_seqs_msams_pid_1306_smacof_points_nj.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhk6MbmJNW1fov0BTOxU52BsnN-RnRQPY2x8cyb84fHCHAjwa3FWAyvL6IzLvMMcuOibAshiLaO6RYVyT7IklfNvpzyy1RbnjoJzdm4D84ee5yj6l-2hn-DcBRKnjyvnCzcjdq_OLKzJvc1/s1600/AMF_Phylo_Seqs_999Nts_Apr17MAFFT_seqs_msams_pid_1306_smacof_points_nj.png" height="207" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="font-size: 13px;">MSA Result</td></tr>
</tbody></table>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiHqmODWd90v6WmG84nwjcTMNs8YG0h9IlycVRdiHJMiuH0eHoUPAqVTot-zI6I5a7I0piGIuHMhOg-zbv0nBiKG7ZAkswD6eVZf3alSZmia3MlPS7NTO3Y5GJRtk6CpiljoPu4E9McVGCj/s1600/AMF_Phylo_Seqs_999Nts_Apr17MAFFT_seqs_swgms_pid_1306_smacof_points_nj.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiHqmODWd90v6WmG84nwjcTMNs8YG0h9IlycVRdiHJMiuH0eHoUPAqVTot-zI6I5a7I0piGIuHMhOg-zbv0nBiKG7ZAkswD6eVZf3alSZmia3MlPS7NTO3Y5GJRtk6CpiljoPu4E9McVGCj/s1600/AMF_Phylo_Seqs_999Nts_Apr17MAFFT_seqs_swgms_pid_1306_smacof_points_nj.png" height="207" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="font-size: 13px;">SWG Result</td></tr>
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Anonymoushttp://www.blogger.com/profile/12376883776057140162noreply@blogger.com0tag:blogger.com,1999:blog-400445772342786430.post-43480123898918135892013-09-08T12:31:00.003-07:002013-09-08T13:44:18.445-07:00Pairwise Distances from MSA Vs Pairwise Local Alignment Distances for Revised 599Nts<span style="background-color: #fefdfa; color: #333333; font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Following heatmap present the correlation between distances computed from multiple sequence alignment (MSA) versus pairwise local alignment for revised 599Nts dataset (MSA is available <a href="https://www.box.com/shared/static/ysa6z5futqs1hoqij1su.fasta">here</a> and sequence file is <a href="https://www.box.com/shared/static/g51cb2nvtj9225snu2wm.fasta">here</a>).</span><br />
<span style="background-color: #fefdfa; color: #333333; font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span>
<span style="background-color: #fefdfa; color: #333333; font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Details on MSA based distance computation is at </span><a href="http://salsafungiphy.blogspot.com/2013/06/pairwise-distance-calculation.html">http://salsafungiphy.blogspot.com/2013/06/pairwise-distance-calculation.html</a><br />
<span style="background-color: #fefdfa; color: #333333; font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span>
<span style="background-color: #fefdfa; color: #333333; font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;">Details on pairwise local alignment based distance computation is at </span><a href="http://salsafungiphy.blogspot.com/2012/10/pairwise-distances-from-multiple.html">http://salsafungiphy.blogspot.com/2012/10/pairwise-distances-from-multiple.html</a><br />
<span style="background-color: #fefdfa; color: #333333; font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEguI99Z2opJ05jgTMSkyR73cNHbnInIp69MmQdB0ZXeq7XomuXulyNk02C9QuWdYip4A8RyG8V50aHylsBv3Pghv5-YXN99NjvZy9v050RXYTyh6jboSVZLDnnTp5eRaokSb6Nc9f5Y_44/s1600/whole-plot-MSAStrictPIDNG-Vs-SWGPIDDensitySat%5B0.85%5D-large.png" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEguI99Z2opJ05jgTMSkyR73cNHbnInIp69MmQdB0ZXeq7XomuXulyNk02C9QuWdYip4A8RyG8V50aHylsBv3Pghv5-YXN99NjvZy9v050RXYTyh6jboSVZLDnnTp5eRaokSb6Nc9f5Y_44/s640/whole-plot-MSAStrictPIDNG-Vs-SWGPIDDensitySat%5B0.85%5D-large.png" width="640" /></a></div>
<span style="background-color: #fefdfa; color: #333333; font-family: Arial, Tahoma, Helvetica, FreeSans, sans-serif; font-size: 13px; line-height: 18px;"><br /></span>Saliya Ekanayakehttp://www.blogger.com/profile/10281589417412608237noreply@blogger.com0tag:blogger.com,1999:blog-400445772342786430.post-10537223367040428042013-09-04T22:28:00.000-07:002013-09-04T22:29:42.308-07:00Summary of Multi-Dimensional Scaling Runs<iframe allowfullscreen="true" frameborder="0" height="749" mozallowfullscreen="true" src="https://docs.google.com/presentation/d/11z7Z3Zw01iORAw66ApCLYi2aRhk7jdJcprY5f4pMHkc/embed?start=false&loop=false&delayms=3000" webkitallowfullscreen="true" width="960"></iframe>Saliya Ekanayakehttp://www.blogger.com/profile/10281589417412608237noreply@blogger.com0tag:blogger.com,1999:blog-400445772342786430.post-83149984225644704072013-06-17T09:21:00.000-07:002013-06-17T09:27:10.003-07:00Pairwise Distances from Multiple Sequence Alignment (MSA) Vs Pairwise Local Alignment DistancesFollowing heatmaps present the correlation between distances computed from multiple sequence alignment (MSA) versus pairwise local alignment. Distance computation from MSA is explained in the previous post at <a href="http://salsafungiphy.blogspot.com/2013/06/pairwise-distance-calculation.html">http://salsafungiphy.blogspot.com/2013/06/pairwise-distance-calculation.html</a>. Distances computed from pairwise local alignment follows the usual recipe of using Smith-Waterman with -16/-4 gap penalties and EDNAFULL scoring matrix for alignment followed by percent identity based distance computation. A similar study was done with previous data as well (see <a href="http://salsafungiphy.blogspot.com/2012/10/pairwise-distances-from-multiple.html">http://salsafungiphy.blogspot.com/2012/10/pairwise-distances-from-multiple.html</a>).<br />
<br />
<br />
<ul>
<li>599Nts data set</li>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjmsn4L9ZRq8llzfqBJqZo4-CdBluA-jxDaBmkQO9qv9z8m3pqRu4jEVFzX2RCpycgtz4EyAlz8mDf04qIu_TN5SBiKCf59me092sFNivgDw-iDwzIaapTs4prjYyNzpGxKmcTR8lshphQ/s1600/whole-plot-MSAStrictPIDNG-Vs-SWGPIDDensitySat%5B0.85%5D-large.png" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjmsn4L9ZRq8llzfqBJqZo4-CdBluA-jxDaBmkQO9qv9z8m3pqRu4jEVFzX2RCpycgtz4EyAlz8mDf04qIu_TN5SBiKCf59me092sFNivgDw-iDwzIaapTs4prjYyNzpGxKmcTR8lshphQ/s640/whole-plot-MSAStrictPIDNG-Vs-SWGPIDDensitySat%5B0.85%5D-large.png" width="640" /></a><br />
</ul>
<br />
<br />
<br />
<ul>
<li>999Nts data set</li>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjTGee4-8crgLkFjtkrOzVWBG0N5ARIHgA_sQ56sWt_sbVyRYsQ5mjzDcMtIb93lLqWInNzCUNOrqVpA34hOKH_yASPil7QU7ahNbbtwgwJns2CFCvpE5zBkp0oDiTVIeQdijvazvZNogw/s1600/whole-plot-MSAStrictPIDNG-Vs-SWGPIDDensitySat%5B0.85%5D-large.png" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjTGee4-8crgLkFjtkrOzVWBG0N5ARIHgA_sQ56sWt_sbVyRYsQ5mjzDcMtIb93lLqWInNzCUNOrqVpA34hOKH_yASPil7QU7ahNbbtwgwJns2CFCvpE5zBkp0oDiTVIeQdijvazvZNogw/s640/whole-plot-MSAStrictPIDNG-Vs-SWGPIDDensitySat%5B0.85%5D-large.png" width="640" /></a><br />
</ul>
Saliya Ekanayakehttp://www.blogger.com/profile/10281589417412608237noreply@blogger.com0tag:blogger.com,1999:blog-400445772342786430.post-23011721356526279402013-06-06T13:03:00.000-07:002013-06-06T13:07:51.547-07:00Pairwise Distance CalculationDistance between each pair of sequences is the input for our algorithms performing dimensional scaling and clustering. The usual form of distance we've been using is to compute percent identity as described <a href="http://salsafungiphy.blogspot.com/2012/10/pairwise-distances-from-multiple.html">here</a>. However, since the sequences are already aligned with respect to each other, our collaborators were interested in computing pairwise distance from multiple sequence alignment (MSA) itself based on the following strategy. Apparently, this is identical to the method we've been adopting previously, known as PIDNG with Strict DNA Alphabet in <a href="http://salsafungiphy.blogspot.com/2012/10/pairwise-distances-from-multiple.html">here</a>.<br />
<br />
The following content is copied from the email sent by Geoffrey House.<br />
<br />
<hr />
<div class="MsoNormal">
<span style="font-family: Courier; font-size: 14.0pt;">Pairwise
gap deletion strategy for AMF clustering project<o:p></o:p></span></div>
<div class="MsoNormal">
<span style="font-family: Courier; font-size: 14.0pt;">May 21,
2013<o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="background: yellow; font-family: Courier; font-size: 14.0pt; mso-highlight: yellow;">Yellow highlight – Same base; base
position <a href="http://www.blogger.com/blogger.g?blogID=400445772342786430" name="OLE_LINK6"></a><a href="http://www.blogger.com/blogger.g?blogID=400445772342786430" name="OLE_LINK5"><b><u>is</u></b></a>
counted in length</span><span style="font-family: Courier; font-size: 14.0pt;"><o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="background: red; font-family: Courier; font-size: 14.0pt; mso-highlight: red;">Red highlight – Different base; base position
<b><u>is</u></b> counted in length</span><span style="font-family: Courier; font-size: 14.0pt;"><o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="background: lime; font-family: Courier; font-size: 14.0pt; mso-highlight: lime;">Green highlight – <a href="http://www.blogger.com/blogger.g?blogID=400445772342786430" name="OLE_LINK4"></a><a href="http://www.blogger.com/blogger.g?blogID=400445772342786430" name="OLE_LINK3"></a><a href="http://www.blogger.com/blogger.g?blogID=400445772342786430" name="OLE_LINK8"></a><a href="http://www.blogger.com/blogger.g?blogID=400445772342786430" name="OLE_LINK7">Skip this position (there is a gap in one or
both of the sequences); base position <b><u>not</u></b>
counted in length</a></span><span style="font-family: Courier; font-size: 14.0pt;"><o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="background: fuchsia; font-family: Courier; font-size: 14.0pt; mso-highlight: fuchsia;">Pink highlight - Skip this position
(there is an ambiguous nucleotide in one or both of the sequences); base
position <b><u>not</u></b> counted in
length</span><span style="font-family: Courier; font-size: 14.0pt;"><o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="font-family: Courier; font-size: 14.0pt;">Sequence
1: <a href="http://www.blogger.com/blogger.g?blogID=400445772342786430" name="OLE_LINK2"></a><a href="http://www.blogger.com/blogger.g?blogID=400445772342786430" name="OLE_LINK1"></a><a href="http://www.blogger.com/blogger.g?blogID=400445772342786430" name="OLE_LINK12"></a><a href="http://www.blogger.com/blogger.g?blogID=400445772342786430" name="OLE_LINK11">-ATG---WCT</a><o:p></o:p></span></div>
<div class="MsoNormal">
<span style="font-family: Courier; font-size: 14.0pt;">Sequence 2: <a href="http://www.blogger.com/blogger.g?blogID=400445772342786430" name="OLE_LINK18"></a><a href="http://www.blogger.com/blogger.g?blogID=400445772342786430" name="OLE_LINK17">-TTGC--W-A<o:p></o:p></a></span></div>
<div class="MsoNormal">
<span style="font-family: Courier; font-size: 14.0pt;">Sequence
3: <a href="http://www.blogger.com/blogger.g?blogID=400445772342786430" name="OLE_LINK14"></a><a href="http://www.blogger.com/blogger.g?blogID=400445772342786430" name="OLE_LINK13">GATGY---GT</a><o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<a href="http://www.blogger.com/blogger.g?blogID=400445772342786430" name="OLE_LINK10"></a><a href="http://www.blogger.com/blogger.g?blogID=400445772342786430" name="OLE_LINK9"><span style="font-family: Courier; font-size: 14.0pt;">Pairwise
comparison 1 between sequences 1 and 2 (the length of the comparison is 4; 2
base positions are different):</span></a><span style="font-family: Courier; font-size: 14.0pt;"><o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="background: lime; font-family: Courier; font-size: 14.0pt; mso-highlight: lime;">-</span><span style="background: red; font-family: Courier; font-size: 14.0pt; mso-highlight: red;">A</span><span style="background: yellow; font-family: Courier; font-size: 14.0pt; mso-highlight: yellow;">TG</span><span style="background: lime; font-family: Courier; font-size: 14.0pt; mso-highlight: lime;">---</span><span style="background: fuchsia; font-family: Courier; font-size: 14.0pt; mso-highlight: fuchsia;">W</span><span style="background: lime; font-family: Courier; font-size: 14.0pt; mso-highlight: lime;">C</span><span style="background: red; font-family: Courier; font-size: 14.0pt; mso-highlight: red;">T</span><span style="font-family: Courier; font-size: 14.0pt;"><o:p></o:p></span></div>
<div class="MsoNormal">
<span style="background: lime; font-family: Courier; font-size: 14.0pt; mso-highlight: lime;">-</span><span style="background: red; font-family: Courier; font-size: 14.0pt; mso-highlight: red;">T</span><span style="background: yellow; font-family: Courier; font-size: 14.0pt; mso-highlight: yellow;">TG</span><span style="background: lime; font-family: Courier; font-size: 14.0pt; mso-highlight: lime;">C--</span><span style="background: fuchsia; font-family: Courier; font-size: 14.0pt; mso-highlight: fuchsia;">W</span><span style="background: lime; font-family: Courier; font-size: 14.0pt; mso-highlight: lime;">-</span><span style="background: red; font-family: Courier; font-size: 14.0pt; mso-highlight: red;">A</span><span style="font-family: Courier; font-size: 14.0pt;"><o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<a href="http://www.blogger.com/blogger.g?blogID=400445772342786430" name="OLE_LINK16"></a><a href="http://www.blogger.com/blogger.g?blogID=400445772342786430" name="OLE_LINK15"><span style="font-family: Courier; font-size: 14.0pt;">Pairwise
comparison 2 between sequences 1 and 3 (the length of the comparison is 5; 1
base position is different):<o:p></o:p></span></a></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="background: lime; font-family: Courier; font-size: 14.0pt; mso-highlight: lime;">-</span><span style="background: yellow; font-family: Courier; font-size: 14.0pt; mso-highlight: yellow;">ATG</span><span style="background: lime; font-family: Courier; font-size: 14.0pt; mso-highlight: lime;">---</span><span style="background: fuchsia; font-family: Courier; font-size: 14.0pt; mso-highlight: fuchsia;">W</span><span style="background: red; font-family: Courier; font-size: 14.0pt; mso-highlight: red;">C</span><span style="background: yellow; font-family: Courier; font-size: 14.0pt; mso-highlight: yellow;">T</span><span style="font-family: Courier; font-size: 14.0pt;"><o:p></o:p></span></div>
<div class="MsoNormal">
<span style="background: lime; font-family: Courier; font-size: 14.0pt; mso-highlight: lime;">G</span><span style="background: yellow; font-family: Courier; font-size: 14.0pt; mso-highlight: yellow;">ATG</span><span style="background: fuchsia; font-family: Courier; font-size: 14.0pt; mso-highlight: fuchsia;">Y</span><span style="background: lime; font-family: Courier; font-size: 14.0pt; mso-highlight: lime;">---</span><span style="background: red; font-family: Courier; font-size: 14.0pt; mso-highlight: red;">G</span><span style="background: yellow; font-family: Courier; font-size: 14.0pt; mso-highlight: yellow;">T</span><span style="font-family: Courier; font-size: 14.0pt;"><o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="font-family: Courier; font-size: 14.0pt;">Pairwise
comparison 3 between sequences 2 and 3 (the length of the comparison is 4; 2
base positions is different):<o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="background: lime; font-family: Courier; font-size: 14.0pt; mso-highlight: lime;">-</span><span style="background: red; font-family: Courier; font-size: 14.0pt; mso-highlight: red;">T</span><span style="background: yellow; font-family: Courier; font-size: 14.0pt; mso-highlight: yellow;">TG</span><span style="background: fuchsia; font-family: Courier; font-size: 14.0pt; mso-highlight: fuchsia;">C</span><span style="background: lime; font-family: Courier; font-size: 14.0pt; mso-highlight: lime;">--</span><span style="background: fuchsia; font-family: Courier; font-size: 14.0pt; mso-highlight: fuchsia;">W</span><span style="background: lime; font-family: Courier; font-size: 14.0pt; mso-highlight: lime;">-</span><span style="background: red; font-family: Courier; font-size: 14.0pt; mso-highlight: red;">A</span><span style="font-family: Courier; font-size: 14.0pt;"><o:p></o:p></span></div>
<br />
<div class="MsoNormal">
<span style="background: lime; font-family: Courier; font-size: 14.0pt; mso-highlight: lime;">G</span><span style="background: red; font-family: Courier; font-size: 14.0pt; mso-highlight: red;">A</span><span style="background: yellow; font-family: Courier; font-size: 14.0pt; mso-highlight: yellow;">TG</span><span style="background: fuchsia; font-family: Courier; font-size: 14.0pt; mso-highlight: fuchsia;">Y</span><span style="background: lime; font-family: Courier; font-size: 14.0pt; mso-highlight: lime;">---G</span><span style="background: red; font-family: Courier; font-size: 14.0pt; mso-highlight: red;">T</span><span style="font-family: Courier; font-size: 14.0pt;"><o:p></o:p></span></div>
Saliya Ekanayakehttp://www.blogger.com/profile/10281589417412608237noreply@blogger.com0tag:blogger.com,1999:blog-400445772342786430.post-73873187323494407982013-06-04T08:13:00.000-07:002013-06-06T13:08:11.848-07:00Phase Two of Phylogenetic Work<div style="text-align: justify;">
In this phase we received two sets of refined sequences. The sequences in these sets come from sequences, which we've been denoting as Kruger and Wittiya sequences. Posts on this blog hereupon will be referencing these new data sets unless noted otherwise.<br />
<br />
The sequences are already aligned using multiple sequence alignment and the we name the two data sets as 599Nts and 999Nts as they contain 599 and 999 base spans respectively in the aligned form. Total number of sequences in these sets are,<br />
<br />
<ul>
<li>599Nts -- 1821 sequences</li>
<li>999Nts -- 1306 sequences</li>
</ul>
</div>
<div style="text-align: justify;">
<br />
The description we received from our collaborators on this data is (copied from email conversation with Geoffrey House and modified for blog) is given below on the right with the graph.</div>
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<div style="color: #222222; font-family: arial, sans-serif; font-size: 13.333333969116211px; text-align: justify;">
<br /></div>
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<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgcOYxJBjphsZMbzailOWxVA4jhS3vabiIADx628EkDw6qOv4RhCM8p93ptWFrAVWBj851YQj17hOQ8NPiUjOjYfvGuSLHWFN6BMSINbwT-kP2ey-QQpmfU0dHBcT6bofJjoHuSBTMsQhg/s1600/description.png" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgcOYxJBjphsZMbzailOWxVA4jhS3vabiIADx628EkDw6qOv4RhCM8p93ptWFrAVWBj851YQj17hOQ8NPiUjOjYfvGuSLHWFN6BMSINbwT-kP2ey-QQpmfU0dHBcT6bofJjoHuSBTMsQhg/s1600/description.png" /></a></div>
<div style="color: #222222; font-family: arial, sans-serif; font-size: 13.333333969116211px; text-align: justify;">
<i style="font-size: 13.333333969116211px;"><br /></i></div>
<div style="color: #222222; font-family: arial, sans-serif; font-size: 13.333333969116211px; text-align: justify;">
<i style="font-size: 13.333333969116211px;"><br /></i></div>
<div>
<div style="color: #222222; font-family: arial, sans-serif; font-size: 13.333333969116211px; text-align: justify;">
<i style="font-size: 13.333333969116211px;">We created the full sequence data set (for the large subunit (LSU) sequences only) by taking the aligned sequences that were used in Kruger et al 2012 (and that were 400-1300 bp long), and adding Wittaya's sequences to the existing alignment using MAFFT and its --add option.</i></div>
<div style="color: #222222; font-family: arial, sans-serif; font-size: 13px; font-style: italic; text-align: justify;">
<br /></div>
</div>
<div style="color: #222222; font-family: arial, sans-serif; font-size: 13.333333969116211px; text-align: justify;">
<i style="font-size: 13.333333969116211px;">We then made line graphs of the number of sequences that contained a base at each sequence position </i><i style="font-size: 13.333333969116211px;">T</i><i style="font-size: 13.333333969116211px;">he top panel is the sequence coverage of the combined data set (Kruger and Wittaya), the middle panel graphs the sequence coverage of only the Kruger sequences within the combined data set, and the bottom panel graphs the sequence coverage of only the Wittaya sequences within the combined data set. </i></div>
<div style="font-style: italic; text-align: justify;">
<span style="color: #222222; font-family: arial, sans-serif; font-size: 13px;"><br /></span></div>
<span style="color: #222222; font-family: arial, sans-serif; font-size: 13.333333969116211px; font-style: italic;"></span><br />
<div style="text-align: justify;">
<span style="color: #222222; font-family: arial, sans-serif; font-size: 13.333333969116211px; font-style: italic;"><i><span style="font-size: 13.333333969116211px;">From the graphs, we saw that a large number of sequences contained nucleotides along a 999 base span. Even more sequences contained nucleotides along a 499 base span that was nested within the 999 base span. The red rectangles above the top panel of the graph to denote the approximate sequence locations of these two different base length spans. </span></i></span></div>
<span style="color: #222222; font-family: arial, sans-serif; font-size: 13.333333969116211px; font-style: italic;">
</span>
<div style="font-style: italic; text-align: justify;">
<br /></div>
<span style="color: #222222; font-family: arial, sans-serif; font-size: 13.333333969116211px; font-style: italic;"></span><br />
<div style="text-align: justify;">
<span style="color: #222222; font-family: arial, sans-serif; font-size: 13.333333969116211px; font-style: italic;"><i><span style="font-size: 13.333333969116211px;">This is how we derived the two sets of sequences - one is all of the sequences that span the 499 bases, and the other is all of the sequences that span the 999 bases (which essentially represents a subset of the sequences spanning the 499 base length).</span></i></span></div>
<span style="color: #222222; font-family: arial, sans-serif; font-size: 13.333333969116211px; font-style: italic;">
</span>
<div style="font-style: italic; text-align: justify;">
<br /></div>
</div>
<div style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13.333333969116211px; text-align: justify;">
<i>Finally for adding Wittaya's sequences to Kruger's, we used the default alignment option in MAFFT, which is very fast but possibly a bit rough. It is possible that we may need to slightly refine the MAFFT alignments later in the project to improve their accuracy, but that should have a fairly small effect on the length of the aligned sequences.</i></div>
Saliya Ekanayakehttp://www.blogger.com/profile/10281589417412608237noreply@blogger.com0tag:blogger.com,1999:blog-400445772342786430.post-7680664635740176892012-11-28T23:20:00.001-08:002012-11-28T23:20:59.973-08:00Robinson-Foulds Distances<p>Here we present the Robinson-Foulds metric computed for trees with 2133 and 200 Fungi taxa. Details on these datasets are presented at <a title="http://salsafungiphy.blogspot.com/2012/11/tree-distance-heatmaps.html" href="http://salsafungiphy.blogspot.com/2012/11/tree-distance-heatmaps.html">http://salsafungiphy.blogspot.com/2012/11/tree-distance-heatmaps.html</a></p> <h1>Metric for Fungi 2133</h1> <p>We have following five trees generated with this dataset.</p> <ul> <li>Tree A <ul> <li>Pairwise sequence alignment with Smith-Waterman algorithm using EDNAFULL scoring matrix and gap penalties –16 and –4 for gap open and gap extension respectively. <li>Distance measure between sequences is percent identity <li>Tree created with Ninja</li></ul> <li>Tree B <ul> <li>Multiple sequence alignment with MUSCLE <li>Tree created with RAxML</li></ul> <li>Tree C <ul> <li>Distance between sequences are taken as the <strong>3D</strong> distance resulted from DA-SMACOF dimensional scaling of the Smith-Waterman percent identity distances (used in Tree A). <li>Tree created with Ninja</li></ul> <li>Tree D <ul> <li>Distance between sequences are taken as the <strong>10D</strong> distance resulted from Manxcat (dimensional scaling program) running in SMACOF mode for the Smith-Waterman percent identity distances (used in Tree A). <li>Tree created with Ninja</li></ul> <li>Tree E <ul> <li>Distance between sequences are taken as the <strong>10D</strong> distance resulted from DA-SMACOF dimensional scaling of the Smith-Waterman percent identity distances (used in Tree A). <li>Tree created with Ninja</li></ul></li></ul> <h2>Robinson-Foulds metric for trees</h2> <ul> <li>The metric is computed with PHYLIP package found at <a title="http://evolution.genetics.washington.edu/phylip.html" href="http://evolution.genetics.washington.edu/phylip.html">http://evolution.genetics.washington.edu/phylip.html</a></li></ul> <table border="0" cellspacing="0" cellpadding="2" width="400"> <tbody> <tr> <td valign="top" width="66"> </td> <td valign="top" width="66"> <p align="center">Tree A</p></td> <td valign="top" width="66"> <p align="center">Tree B</p></td> <td valign="top" width="66"> <p align="center">Tree C</p></td> <td valign="top" width="66"> <p align="center">Tree D</p></td> <td valign="top" width="66"> <p align="center">Tree E</p></td></tr> <tr> <td valign="top" width="66"> <p align="center">Tree A</p></td> <td valign="top" width="66"> <p align="center">0</p></td> <td valign="top" width="66"> <p align="center">3484 </p></td> <td valign="top" width="66"> <p align="center">3966 </p></td> <td valign="top" width="66"> <p align="center">3726 </p></td> <td valign="top" width="66"> <p align="center">3740 </p></td></tr> <tr> <td valign="top" width="66"> <p align="center">Tree B</p></td> <td valign="top" width="66"> <p align="center">3484 </p></td> <td valign="top" width="66"> <p align="center">0</p></td> <td valign="top" width="66"> <p align="center">3956 </p></td> <td valign="top" width="66"> <p align="center">3796 </p></td> <td valign="top" width="66"> <p align="center">3806 </p></td></tr> <tr> <td valign="top" width="66"> <p align="center">Tree C</p></td> <td valign="top" width="66"> <p align="center">3966 </p></td> <td valign="top" width="66"> <p align="center">3956 </p></td> <td valign="top" width="66"> <p align="center">0</p></td> <td valign="top" width="66"> <p align="center">3438 </p></td> <td valign="top" width="66"> <p align="center">3392 </p></td></tr> <tr> <td valign="top" width="66"> <p align="center">Tree D</p></td> <td valign="top" width="66"> <p align="center">3726 </p></td> <td valign="top" width="66"> <p align="center">3796 </p></td> <td valign="top" width="66"> <p align="center">3438 </p></td> <td valign="top" width="66"> <p align="center">0</p></td> <td valign="top" width="66"> <p align="center">1282 </p></td></tr> <tr> <td valign="top" width="66"> <p align="center">Tree E</p></td> <td valign="top" width="66"> <p align="center">3740 </p></td> <td valign="top" width="66"> <p align="center">3806 </p></td> <td valign="top" width="66"> <p align="center">3392 </p></td> <td valign="top" width="66"> <p align="center">1282 </p></td> <td valign="top" width="66"> <p align="center">0</p></td></tr></tbody></table> <ul> <ul> <ul> <p> </p></ul></ul></ul> Saliya Ekanayakehttp://www.blogger.com/profile/10281589417412608237noreply@blogger.com0tag:blogger.com,1999:blog-400445772342786430.post-70814689022047639262012-11-28T22:34:00.001-08:002014-08-24T13:22:47.120-07:00Phylogenetic Tree Mega Table<h3>
Introduction</h3>
<div>
Here we present the summary of our work related with phylogenetic tree
creation and visualization of Fungi data. The experiments were carried out
primarily on two data sets, which we name as <em>Fungi 200</em> and <em>Fungi
2133. </em>Details of these data sets are as follows.<br />
<h3>
</h3>
<h4>
</h4>
<h4>
Fungi 200</h4>
<ul>
<li>FASTA file is available at <a href="https://www.sugarsync.com/pf/D6858752_2739277_6854163">https://www.sugarsync.com/pf/D6858752_2739277_6854163</a></li>
<li>126 sequences (in reverse complemented form) represent the centers for
clusters in <a href="http://salsahpc.indiana.edu/millionseq/fungi/fungi_index.html">http://salsahpc.indiana.edu/millionseq/fungi/fungi_index.html</a>
(note. restricted access). Indices from 0 to 125 inclusive
</li>
<li>74 sequences from GenBank. Indices from </li>
</ul>
<h3>
</h3>
<h4>
Fungi 2133 </h4>
<ul>
<li>FASTA file is available at <a href="https://www.sugarsync.com/pf/D6858752_0743775_6281705">https://www.sugarsync.com/pf/D6858752_0743775_6281705</a></li>
<li>126 sequences (in reverse complemented form) represent the centers for
clusters in <a href="http://salsahpc.indiana.edu/millionseq/fungi/fungi_index.html">http://salsahpc.indiana.edu/millionseq/fungi/fungi_index.html</a>
(note. restricted access). Indices from 0 to 125 inclusive
</li>
<li>74 sequences from GenBank. Indices from 126 to 199 inclusive
</li>
<li>988 sequences from Kruger et. al. dataset. Indices from 200 to 1187
inclusive
</li>
<li>945 sequences from Wittiya’s dataset. Indices from 1188 to 2132
inclusive</li>
</ul>
Note on 126 centers:<br />
Originally we had 7 mega-regions in <a href="http://salsahpc.indiana.edu/millionseq/haixu/fungi_index.html">million
sequence</a> clustering project and they had a total of 140 clusters. Each
cluster was represented by three center sequences of which were 126 is picked as
the best.<br />
<br />
<h3>
Links</h3>
Following are links to previous posts on listed topics.<br />
<ol>
<li>The 200 sequence set without tree can be found <a href="http://salsahpc.indiana.edu/PhylogeneticTree/126+74_swg_pid_dasmacof_labeled_grouped.pviz">here</a>. The 2133 sequence set without tree can be found <a href="http://salsahpc.indiana.edu/PhylogeneticTree/2133_swg_pid_dasmacof_labeled_grouped.pviz">here</a>.</li>
<li>A description on tree generation methods is available <a href="http://salsafungiphy.blogspot.com/2012/11/phylogenetic-tree-generation-for.html">here</a>. </li>
<li>Tree quality comparisons of edge sum and correlation are available <a href="http://salsafungiphy.blogspot.com/2012/11/tree-quality-comparison-with-different.html">here</a>.</li>
<li>Heatmap comparisons,</li>
<ul>
<li>pairwise edge sum distance versus other distance measures for leaf nodes is available <a href="http://salsafungiphy.blogspot.com/2012/11/tree-distance-heatmaps.html">here</a>.</li>
<li>pairwise 10D, 3D, and SWG PID distances for leaf nodes is available <a href="http://salsafungiphy.blogspot.com/2012/11/heatmaps-of-10d-vs-3d-vs-swg.html">here</a>.</li>
<li>pairwise normalized score distance measures versus SWG PID is available <a href="http://salsafungiphy.blogspot.com/2012/10/heatmaps-of-different-distances.html">here</a>.</li>
<li>pairwise distance from multiple sequence alignment versus pairwise local alignment is available <a href="http://salsafungiphy.blogspot.com/2012/10/pairwise-distances-from-multiple.html">here</a>.</li>
</ul>
<li>Robinson-Foulds metric for trees is available <a href="http://salsafungiphy.blogspot.com/2012/11/robinson-foulds-distances_28.html">here</a>. (summary of this given below as well)</li>
</ol>
</div>
<h4>
</h4>
<h3>
Column Name Explanation</h3>
<ol>
<li><b>Sequence Set: </b>The two sequence sets as given above.</li>
<li><b>Tree Generation Method:</b> Multiple Sequence Alignment includes Clustal Omega, Clustal W2 and Muscle; Tree Generation includes FastTree, Raxml, Ninja and Neighbor Joining. Neighbor Joining is our implementation of method used in Ninja.</li>
<li><b>Euclidean Mapping (Interpolation Method): </b>Define leaf nodes as the sample set and internal nodes as out-of-sample set. Use leaf node positions in 3D or 10D from MDS. Calculate internal node positions in 3D or 10D respectively by "neighbor joining" formulae in <a href="http://en.wikipedia.org/wiki/Neighbor_joining">wikipedia.</a> However, tree itself is NOT defined necessarily by neighborhood joining but rather using the Tree Generation Method in previous column. Note that either Internal Node Interpolation and Full 3D map are used in Spherical Phylogram in following column.</li>
<ul>
<li><b>Internal Node Interpolation (MI-MDS)</b> was from Majorizing Iterative MDS method: The leaf nodes are fixed from basic MDS on them. Each node position has position calculated iteratively as it is added to the sample.</li>
<li><b>Full 3D map</b><b> </b>uses a full MDS for whole sample but fixes the leaf nodes at positions from their MDS (i.e. in same positions as Internal Node Interpolation). This gives improved results as all internal node mapped positions are varied simultaneously subject to distance matrix.</li>
<ul>
</ul>
</ul>
<li><b>Edge Sum: </b>edge sum is the sum of all the edges' lengths, as in 3D, 10D using Euclidean mapping mentioned above.</li>
<b></b>
<ul>
<li>Calculate tree by method defined in "Tree Generation Method" column and then calculate edge sum by one of three methods defined below. Note each method projects tree to a Euclidean space and uses Neighborhood Joining formulae for distances</li>
</ul>
<ol><ul>
<li>3D (3D) means instantiate tree in 3D and calculate edge sum in 3D, too;</li>
<li>10D (10D) means instantiate tree in 10D and calculate edge sum in 10D, too;</li>
<li>10D (3D) means instantiate tree in 10D and calculate edge sum in 3D after mapping 10D tree into 3D by MDS as described above.</li>
<ul>
</ul>
</ul>
</ol>
<li><b>Stress: </b>same definition as in dimension reduction techniques, calculate the error between target dimension Euclidean pairwise distance matrix to original dimension Eculidean pairwise distance matrix. In our particular calculation, it's the error from 10D to 3D dimension reduction, that error between target 3D and original 10D.</li>
<li><b>Correlation: </b>Simple correlation between leaf sum from newick file (each nodes' contains the distance from it to its direct parent) and original pid distance matrix / 3D plot distance matrix.</li>
<li><b>Plots:</b> <b>Spherical</b> is short for <b>Spherical Phylogram</b>, where it's similar to Circular Phylogram but also consider preserving the correlations among original sequences, the internal nodes are calculated using interpolation; <b>Cuboid</b> is short for <b>Cuboid Cladogram</b>, it's same as for Rectangular Cladogram, but in 3D. The internal nodes are NOT calculated by interpolation, but rather the middle of each pair of it's direct children; <b>Rectangle</b> is short for <b>Rectangular Cladogram</b>, where is generated using Dendroscope.</li>
<li><b>Heatmap</b>
<ul>
<li><b>Edgesum (newick) Vs Original PID</b> compares the correlation of edge sum values versus original PID distance. More information is available at http://salsafungiphy.blogspot.com/2012/11/tree-distance-heatmaps.html</li>
<li><b>MI-MDS Vs Full MDS Mapping </b>compares the correlation of pairwise node distances in trees built from internal node interpolation versus full 3D map.</li>
<li><b>MSA Strict PIDNG Vs SWG PID</b> compares the computed percent identity excluding gaps from multiple sequence alignment versus pairwise Smith-Waterman percent identity distance. Only A, C, T, G characters are considered as the alphabet when computing PIDNG. See more information in http://salsafungiphy.blogspot.com/2012/10/pairwise-distances-from-multiple.html</li>
<li><b>MSA Full PIDNG Vs SWG PID</b> similar to the previous column except <span style="background-color: white; line-height: 18px;"><span style="font-family: inherit;">A, C, M, G, R, S, V, T, W, Y, H, K, D, B, N characters are considered as the alphabet for PIDNG calculation. See more in </span></span><span style="line-height: 17.981481552124023px;">http://salsafungiphy.blogspot.com/2012/10/pairwise-distances-from-multiple.html</span></li>
</ul>
</li>
<li><b>2D View:</b> It's selected screen shot from the 3D plots (in previous column) of Spherical Phylogram or Cuboid Cladogram (made using screen shot feature of 3D viewer <a href="http://salsahpc.indiana.edu/pviz3/">Plotviz</a> running on 3D plots in previous column) plus 2D rectangular cladogram in pdf format.</li>
<br />
<table border="1" style="border-bottom-style: none; border-left-style: none; border-right-style: none; border-top-style: none; font-size: 9pt; width: 1200px;">
<caption>
Mega Information Table for PhyloTree Project
</caption>
<tbody>
<tr>
<th rowspan="2" scope="col" width="8%"><span class="table_head">Sequence Set</span></th>
<th align="center" rowspan="2" scope="col" width="10%"><span class="table_head">Tree Generation Method</span></th>
<th rowspan="2" scope="col" width="6%"><span class="table_head">Euclidean Mapping</span></th>
<th colspan="3" scope="col"><span class="table_head">Edge Sum</span></th>
<th rowspan="2" scope="col" width="4%"><span class="table_head">Stress<br />
10D (3D)</span></th>
<th colspan="2" scope="col"><span class="table_head">Correlation</span><br />
<span class="table_head">Regular Tree</span></th>
<th class="table_head" colspan="4" scope="col">Heat Map </th>
<th rowspan="2" scope="col"><span class="table_head">Plots</span></th>
<th colspan="3" scope="col">2D View</th>
</tr>
<tr>
<td align="center" width="4%"><span class="table_head">3D (3D)</span></td>
<td align="center" width="4%"><span class="table_head">10D (10D)</span></td>
<td align="center" width="3%"><span class="table_head">10D (3D)</span></td>
<td align="center" width="5%"><span class="table_head">With Original Pid</span></td>
<td align="center" width="5%"><span class="table_head">With 3D MDS Map</span></td>
<th class="table_head" scope="col" width="6%">Edge Sum (Newick) vs Origin PID</th>
<th class="table_head" scope="col" width="6%">MI-MDS vs<br />
Full MDS Mapping</th>
<th class="table_head" scope="col" width="6%">MSA Strict PIDNG vs<br />
SWG PID</th>
<th class="table_head" scope="col" width="6%">MSA Full PIDNG vs<br />
SWG PID</th>
<th scope="col">Rectangular Cladogram</th>
<th scope="col">Cuboid Cladogram</th>
<th scope="col">Spherical Phylogram</th>
</tr>
<tr>
<th class="table_head" rowspan="22" scope="row" width="8%">126 + 74 (200) sequences<br />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgXYd1jiuvv_MZymQbGTWWKdAwEla9toNCPYhg-zkSRxnc-vTv3viDScQlO3vZjBWg_NtXBGzgLSY__KeXj261t56HdL7EODtdg_iFQyk7RvUJnUpoZ7XxvxLGIc0FL7EHZ_KGvMVJSyimw/s1600/200_edgeSum.PNG">Edge Sum Comparison Figure</a></th>
<td align="center" class="table_head" rowspan="2" width="10%">1. Clustal Omega FastTree</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="6%">Internal Node Interpolation</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">10.02</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">13.26</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="3%">15.01</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">0.0264</td>
<td align="center" rowspan="2" valign="middle" width="5%">--</td>
<td align="center" rowspan="2" valign="middle" width="5%">--</td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" class="Plots" rowspan="2" valign="middle" width="7%"><a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/qiime/tree_plot/spherical_phylogram/126+74_clustalOmega_fastTree_sp.pviz">Spherical</a><br />
<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/qiime/tree_plot/cuboid_cladogram/126+74_clustalOmega_fastTree_sideTree.pviz">Cuboid</a></td>
<td align="center" rowspan="2" valign="middle" width="6%"><a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/qiime/tree_pdf/126+74_clustalOmega_fastTree.pdf">Rectangle</a></td>
<td align="center" rowspan="2" valign="middle" width="7%"><div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiKexAY4KsABKFnXhHh1vpQB6A9pUMFP1t9lALocBJ0IOq7-kozc3bYLoh2BS2Fd72Q2iAG_ApeIpdluynrQdaFXTEob_MDp1f2Kpdhr3QGaDqA95VRiWLVNlVsGWQJ-jpwMZxoHcaJAg-8/s1600/126+74_clustalOmega_fastTree_sideTree.png" imageanchor="1"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiKexAY4KsABKFnXhHh1vpQB6A9pUMFP1t9lALocBJ0IOq7-kozc3bYLoh2BS2Fd72Q2iAG_ApeIpdluynrQdaFXTEob_MDp1f2Kpdhr3QGaDqA95VRiWLVNlVsGWQJ-jpwMZxoHcaJAg-8/s1600/126+74_clustalOmega_fastTree_sideTree.png" height="50" width="50" /></a></div>
</td>
<td align="center" rowspan="2" valign="middle" width="7%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjXZUEA34SW2Pl-M8bhvV4MgyNN9WWyEjiky-aXJAb65XqlgLj4_DUwXW7eJ_7Fc3AekhEA6MZtT_nGfsvIeKKah8T1wMrvESXlztX8i7dsOK2NuF2IuP0xmvQLyzkKDhl66ipXAv-MKDyN/s1600/200_clustalOmega_fastTree_10dto3d.png" imageanchor="1" style="font-size: medium;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjXZUEA34SW2Pl-M8bhvV4MgyNN9WWyEjiky-aXJAb65XqlgLj4_DUwXW7eJ_7Fc3AekhEA6MZtT_nGfsvIeKKah8T1wMrvESXlztX8i7dsOK2NuF2IuP0xmvQLyzkKDhl66ipXAv-MKDyN/s1600/200_clustalOmega_fastTree_10dto3d.png" height="50" width="50" /></a></td>
</tr>
<tr class="Manxcat">
<td align="center" height="20" width="6%">Full 3D Map</td>
<td align="center" height="20" valign="middle" width="4%"></td>
<td align="center" height="20" valign="middle" width="4%">--</td>
<td align="center" height="20" valign="middle" width="3%">11.29</td>
<td align="center" height="20" valign="middle" width="4%">0.0204</td>
</tr>
<tr>
<td align="center" class="table_head" rowspan="2" width="10%">2. Clustal Omega Raxml</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="6%">Internal Node Interpolation</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">11.33</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">14.62</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="3%">16.15</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">0.0247</td>
<td align="center" rowspan="2" valign="middle" width="5%">0.79</td>
<td align="center" rowspan="2" valign="middle" width="5%">0.749</td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" class="Plots" rowspan="2" valign="middle" width="7%"><a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/qiime/tree_plot/spherical_phylogram/126+74_clustalOmega_raxml_sp.pviz">Spherical</a><br />
<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/qiime/tree_plot/cuboid_cladogram/126+74_clustalOmega_raxml_sideTree.pviz">Cuboid</a></td>
<td align="center" rowspan="2" valign="middle" width="6%"><a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/qiime/tree_pdf/126+74_clustalOmega_raxml.pdf">Rectangle</a></td>
<td align="center" rowspan="2" valign="middle" width="7%"> <a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj5xB6hdGKbxN16JBHANb9bKiwsf0wlhkBReaiTiDznZLM5zdLvu922VSVTp_Vf1-nDXQLg91Z_0sJI8dObvuql0nyv7cIbv3p_sbLACWY03OgR_5MBR8ik0TABNUbVZnYlgz7uNqRqH5hz/s1600/126+74_clustalOmega_raxml_sideTree.png" imageanchor="1"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj5xB6hdGKbxN16JBHANb9bKiwsf0wlhkBReaiTiDznZLM5zdLvu922VSVTp_Vf1-nDXQLg91Z_0sJI8dObvuql0nyv7cIbv3p_sbLACWY03OgR_5MBR8ik0TABNUbVZnYlgz7uNqRqH5hz/s1600/126+74_clustalOmega_raxml_sideTree.png" height="50" width="50" /></a></td>
<td align="center" rowspan="2" valign="middle" width="7%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgjybzEvSCZcrx6eyl7sw8pyliJQRNZC6QhDjV_PAVvleVagBRQI6zz2cMamGHOgOBhgtKSkgCNA7KCWo0ceZCj2fVO_1ukp5vWvnLmuGbsKdhpCVSvaGru6gnIvIuBbtSyQIwYFXKyGk2p/s1600/200_clustalOmega_raxml_10dto3d.png" imageanchor="1" style="font-size: medium;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgjybzEvSCZcrx6eyl7sw8pyliJQRNZC6QhDjV_PAVvleVagBRQI6zz2cMamGHOgOBhgtKSkgCNA7KCWo0ceZCj2fVO_1ukp5vWvnLmuGbsKdhpCVSvaGru6gnIvIuBbtSyQIwYFXKyGk2p/s1600/200_clustalOmega_raxml_10dto3d.png" height="50" width="50" /></a></td>
</tr>
<tr class="Manxcat">
<td align="center" height="20" width="6%">Full 3D Map</td>
<td align="center" height="20" valign="middle" width="4%"></td>
<td align="center" height="20" valign="middle" width="4%">--</td>
<td align="center" height="20" valign="middle" width="3%">13.05</td>
<td align="center" height="20" valign="middle" width="4%">0.02</td>
</tr>
<tr>
<td align="center" class="table_head" rowspan="2" width="10%">3. Clustal W2 FastTree</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="6%">Internal Node Interpolation</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">11.16</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">14.68</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="3%">16.67</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">0.0277</td>
<td align="center" rowspan="2" valign="middle" width="5%">--</td>
<td align="center" rowspan="2" valign="middle" width="5%">--</td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" class="Plots" rowspan="2" valign="middle" width="7%"><a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/qiime/tree_plot/spherical_phylogram/126+74_clustalW2_fastTree_sp.pviz">Spherical </a><br />
<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/qiime/tree_plot/cuboid_cladogram/126+74_clustalW2_fastTree_sideTree.pviz">Cuboid</a></td>
<td align="center" rowspan="2" valign="middle" width="6%"><a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/qiime/tree_pdf/126+74_clustalW2_fastTree.pdf">Rectangle</a></td>
<td align="center" rowspan="2" valign="middle" width="7%"> <a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgrdJtZi2QD1x_G5XQSxRGsElaszYNJx3-RsJ9Ebrmn8bfxuS2G66142MycefH1pGcZbSfLpWlsNC_XjQxjQCMP4JUKAxpsr12XcbNNqd5Jys4T4T4vOgVYwKBrj9zvcxq31C8GyH-0tla_/s1600/126+74_clustalW2_fastTree_sideTree.png" imageanchor="1"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgrdJtZi2QD1x_G5XQSxRGsElaszYNJx3-RsJ9Ebrmn8bfxuS2G66142MycefH1pGcZbSfLpWlsNC_XjQxjQCMP4JUKAxpsr12XcbNNqd5Jys4T4T4vOgVYwKBrj9zvcxq31C8GyH-0tla_/s1600/126+74_clustalW2_fastTree_sideTree.png" height="50" width="50" /></a></td>
<td align="center" rowspan="2" valign="middle" width="7%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjPzpftXUnWnaPVIxBZ41chCaPYRUICFYjXL9vc9g-yj57Uj3e7zs_AAEXM_6fGNNa5-RUhCf-_dDIuyJWT1b2my0ocXr5-KWZjgV2O6gkHz7SnD0ZzUNftxtrA_NtPoOpnVBEhZlxMV87q/s1600/200_clustalW2_fastTree_10dto3d.png" imageanchor="1" style="font-size: medium;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjPzpftXUnWnaPVIxBZ41chCaPYRUICFYjXL9vc9g-yj57Uj3e7zs_AAEXM_6fGNNa5-RUhCf-_dDIuyJWT1b2my0ocXr5-KWZjgV2O6gkHz7SnD0ZzUNftxtrA_NtPoOpnVBEhZlxMV87q/s1600/200_clustalW2_fastTree_10dto3d.png" height="50" width="50" /></a></td>
</tr>
<tr class="Manxcat">
<td align="center" height="20" width="6%">Full 3D Map</td>
<td align="center" height="20" valign="middle" width="4%"></td>
<td align="center" height="20" valign="middle" width="4%">--</td>
<td align="center" height="20" valign="middle" width="3%">13.4</td>
<td align="center" height="20" valign="middle" width="4%">0.0205</td>
</tr>
<tr>
<td align="center" class="table_head" rowspan="2" width="10%">4. Clustal W2 Raxml</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="6%">Internal Node Interpolation</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">11.99</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">15.08</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="3%">16.17</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">0.025</td>
<td align="center" rowspan="2" valign="middle" width="5%">0.825</td>
<td align="center" rowspan="2" valign="middle" width="5%">0.78</td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" class="Plots" rowspan="2" valign="middle" width="7%"><a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/qiime/tree_plot/spherical_phylogram/126+74_clustalW2_raxml_sp.pviz">Spherical </a><br />
<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/qiime/tree_plot/cuboid_cladogram/126+74_clustalW2_raxml_sideTree.pviz">Cuboid</a></td>
<td align="center" rowspan="2" valign="middle" width="6%"><a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/qiime/tree_pdf/126+74_clustalW2_raxml.pdf">Rectangle</a></td>
<td align="center" rowspan="2" valign="middle" width="7%"> <a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiSsQeFoiYMYjIvpIVlcAdWkehaXfr5R5ksMo7GEWPCnc_bibBAqoBacMURPGiK3qxZ4aZ-i7uocFcjNTi-WX_Zh8lymkd-8GktJt7kdxJbjX-WWgNIDmr7jV2p17T1J5psLKVAPqidemRk/s1600/126+74_clustalW2_raxml_sideTree.png" imageanchor="1"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiSsQeFoiYMYjIvpIVlcAdWkehaXfr5R5ksMo7GEWPCnc_bibBAqoBacMURPGiK3qxZ4aZ-i7uocFcjNTi-WX_Zh8lymkd-8GktJt7kdxJbjX-WWgNIDmr7jV2p17T1J5psLKVAPqidemRk/s1600/126+74_clustalW2_raxml_sideTree.png" height="50" width="50" /></a></td>
<td align="center" rowspan="2" valign="middle" width="7%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhhhn8EGTZeuZUi_8Y4UYivSpvIhcb66tOcjGevMhbMGrjRPlnN0XGsECjxt3L0UVdXYYhfCNa-1mCgB9WRadMp6jfW-GZJYUoKH8Ve3SS4V_elC1uLS93UhiO4FVt_LQKDbnEL3pYLr9Sa/s1600/200_clustalW2_raxml_10dto3d.png" imageanchor="1" style="font-size: medium;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhhhn8EGTZeuZUi_8Y4UYivSpvIhcb66tOcjGevMhbMGrjRPlnN0XGsECjxt3L0UVdXYYhfCNa-1mCgB9WRadMp6jfW-GZJYUoKH8Ve3SS4V_elC1uLS93UhiO4FVt_LQKDbnEL3pYLr9Sa/s1600/200_clustalW2_raxml_10dto3d.png" height="50" width="50" /></a></td>
</tr>
<tr class="Manxcat">
<td align="center" height="20" width="6%">Full 3D Map</td>
<td align="center" height="20" valign="middle" width="4%"></td>
<td align="center" height="20" valign="middle" width="4%">--</td>
<td align="center" height="20" valign="middle" width="3%">13.69</td>
<td align="center" height="20" valign="middle" width="4%">0.0201</td>
</tr>
<tr>
<td align="center" class="table_head" rowspan="2" width="10%">5. Muscle FastTree</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="6%">Internal Node Interpolation</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">10.61</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">13.8</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="3%">15.79</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">0.0274</td>
<td align="center" rowspan="2" valign="middle" width="5%">--</td>
<td align="center" rowspan="2" valign="middle" width="5%">--</td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" class="Plots" rowspan="2" valign="middle" width="7%"> <a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/qiime/tree_plot/spherical_phylogram/126+74_muscle_fastTree_sp.pviz">Spherical </a><br />
<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/qiime/tree_plot/cuboid_cladogram/126+74_muscle_fastTree_sideTree.pviz">Cuboid</a></td>
<td align="center" rowspan="2" valign="middle" width="6%"><a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/qiime/tree_pdf/126+74_muscle_fastTree.pdf">Rectangle</a></td>
<td align="center" rowspan="2" valign="middle" width="7%"> <a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi_4FkojNKaNQUeiQvbByvs3dQ1P_llepcYrWHUMVPhbwaHD2oOlVpC15bS938TSRQe_ClTWLKrvatPQtLQiuMvNvQ0ySYYxKnXqkSkyCElTUs0WomF1J2eaoyadPjB_P7DayJ5-hJfQqbC/s1600/126+74_muscle_fastTree_sideTree.png" imageanchor="1"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi_4FkojNKaNQUeiQvbByvs3dQ1P_llepcYrWHUMVPhbwaHD2oOlVpC15bS938TSRQe_ClTWLKrvatPQtLQiuMvNvQ0ySYYxKnXqkSkyCElTUs0WomF1J2eaoyadPjB_P7DayJ5-hJfQqbC/s1600/126+74_muscle_fastTree_sideTree.png" height="50" width="50" /></a></td>
<td align="center" rowspan="2" valign="middle" width="7%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhF1IzcfV5pPLTyk-woE4jhNZ702WeakBPUTNMZa_RazkW9rPQLMjB9fg6HFL7jQVfoM1IMjdxEhmcrWUEp4peW23Y7HVBoh_iG5QG8HGSMAjNbn0liuZGljoD9GsUyvh3TqOCjf9X2Jw9t/s1600/200_muscle_fastTree_10dto3d.png" imageanchor="1" style="font-size: medium;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhF1IzcfV5pPLTyk-woE4jhNZ702WeakBPUTNMZa_RazkW9rPQLMjB9fg6HFL7jQVfoM1IMjdxEhmcrWUEp4peW23Y7HVBoh_iG5QG8HGSMAjNbn0liuZGljoD9GsUyvh3TqOCjf9X2Jw9t/s1600/200_muscle_fastTree_10dto3d.png" height="50" width="50" /></a></td>
</tr>
<tr class="Manxcat">
<td align="center" height="20" width="6%">Full 3D Map</td>
<td align="center" height="20" valign="middle" width="4%"></td>
<td align="center" height="20" valign="middle" width="4%">--</td>
<td align="center" height="20" valign="middle" width="3%">12.31</td>
<td align="center" height="20" valign="middle" width="4%">0.0202</td>
</tr>
<tr>
<td align="center" class="table_head" rowspan="2" width="10%">6. Muscle Raxml</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="6%">Internal Node Interpolation</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">10.90</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">14.67</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="3%">16.44</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">0.027</td>
<td align="center" rowspan="2" valign="middle" width="5%">0.823</td>
<td align="center" rowspan="2" valign="middle" width="5%">0.775</td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" class="Plots" rowspan="2" valign="middle" width="7%"><a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/qiime/tree_plot/spherical_phylogram/126+74_muscle_raxml_sp.pviz">Spherical </a><br />
<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/qiime/tree_plot/cuboid_cladogram/126+74_muscle_raxml_sideTree.pviz">Cuboid</a></td>
<td align="center" rowspan="2" valign="middle" width="6%"><a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/qiime/tree_pdf/126+74_muscle_raxml.pdf">Rectangle</a></td>
<td align="center" rowspan="2" valign="middle" width="7%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiGNx-dlaoAart2R3b1lCMBIPRTVLPyr92w2Ox10dP_4tTdgH19CIIl9xvA7bAaASxiXRE0ISivyqQbq8yso-ccaE8bY7-Tn608UWPTySrdDurtOWwtJ86Hcvf9J3LmncTSq8O4yEaTRf30/s1600/126+74_muscle_raxml_sideTree_reroot_newColor.png" imageanchor="1"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiGNx-dlaoAart2R3b1lCMBIPRTVLPyr92w2Ox10dP_4tTdgH19CIIl9xvA7bAaASxiXRE0ISivyqQbq8yso-ccaE8bY7-Tn608UWPTySrdDurtOWwtJ86Hcvf9J3LmncTSq8O4yEaTRf30/s1600/126+74_muscle_raxml_sideTree_reroot_newColor.png" height="50" width="50" /></a> </td>
<td align="center" rowspan="2" valign="middle" width="7%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjGThCL9KA3Su4u73fW9HqsnZpmACic8jbp22y_A226JYgK8BY3-OqdC2XuE8_4vhi6EyfsuLN4bom_FpxpMdBleLXsuVIFUYkqriM3PeKsuwcl1VBY6aW4QzUS_lo8BPvZPrfu8MUoEnD0/s1600/200_muscle_raxml_10dto3d.png" style="font-size: medium;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjGThCL9KA3Su4u73fW9HqsnZpmACic8jbp22y_A226JYgK8BY3-OqdC2XuE8_4vhi6EyfsuLN4bom_FpxpMdBleLXsuVIFUYkqriM3PeKsuwcl1VBY6aW4QzUS_lo8BPvZPrfu8MUoEnD0/s1600/200_muscle_raxml_10dto3d.png" height="50" width="50" /></a></td>
</tr>
<tr class="Manxcat">
<td align="center" height="20" width="6%">Full 3D Map</td>
<td align="center" height="20" valign="middle" width="4%"><br /></td>
<td align="center" height="20" valign="middle" width="4%">--</td>
<td align="center" height="20" valign="middle" width="3%">12.95</td>
<td align="center" height="20" valign="middle" width="4%">0.0202</td>
</tr>
<tr>
<td align="center" class="table_head" rowspan="2" width="10%">7. Neighbor Joining 3D</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="6%">Internal Node Interpolation</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">7.32</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">13.35</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="3%">--</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">--</td>
<td align="center" rowspan="2" valign="middle" width="5%">--</td>
<td align="center" rowspan="2" valign="middle" width="5%">--</td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%">n/a</td>
<td align="center" rowspan="2" valign="middle" width="6%">n/a</td>
<td align="center" class="Plots" rowspan="2" valign="middle" width="7%"><a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/nj/tree_plot/circular_phylogram/126+74_swg_pid_dasmacof_3DplotDistance_nj_cp.pviz">Spherical</a></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="7%">--</td>
<td align="center" rowspan="2" valign="middle" width="7%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgyUvkxUOYslXbCPu4yI2FeygHzyteQwodhxSvIwrgOT51Ag0KkRLqaDM0Wr4z5WoK5a8Vs8tTrnCfP7YqmGH-2XC2JJOWhZjJcR3lYKFfeUWR2zcjEbhIXYc5Ic0VDicDWaum3AB-gHHuf/s1600/126%252B74_swg_pid_dasmacof_3DplotDistance_nj_cp.png" imageanchor="1" style="font-size: medium;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgyUvkxUOYslXbCPu4yI2FeygHzyteQwodhxSvIwrgOT51Ag0KkRLqaDM0Wr4z5WoK5a8Vs8tTrnCfP7YqmGH-2XC2JJOWhZjJcR3lYKFfeUWR2zcjEbhIXYc5Ic0VDicDWaum3AB-gHHuf/s1600/126%252B74_swg_pid_dasmacof_3DplotDistance_nj_cp.png" height="50" width="50" /></a></td>
</tr>
<tr class="Manxcat">
<td align="center" height="20" width="6%">Full 3D Map</td>
<td align="center" height="20" valign="middle" width="4%">7.33</td>
<td align="center" height="20" valign="middle" width="4%">--</td>
<td align="center" height="20" valign="middle" width="3%">--</td>
<td align="center" height="20" valign="middle" width="4%">--</td>
</tr>
<tr>
<td align="center" class="table_head" rowspan="2" width="10%">8. Ninja 3D plot</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="6%">Internal Node Interpolation</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">7.36</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">12.92</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="3%">14.51</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">0.0268</td>
<td align="center" rowspan="2" valign="middle" width="5%">0.787</td>
<td align="center" rowspan="2" valign="middle" width="5%">0.774</td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%">n/a</td>
<td align="center" rowspan="2" valign="middle" width="6%">n/a</td>
<td align="center" class="Plots" rowspan="2" valign="middle" width="7%"><a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/mega_table_plots/200/spherical_phylogram/manxcat/200_ninja3d_10dto3d.pviz">Spherical</a><br />
<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/mega_table_plots/200/cuboid_cladogram/126+74_3dmap_ninja.pviz">Cuboid</a></td>
<td align="center" rowspan="2" valign="middle" width="6%"><a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/mega_table_plots/200/rectangular_cladogram/126+74_swg_pid_dasmacof_labeled_1_3d_dist.pdf">Rectangle</a></td>
<td align="center" rowspan="2" valign="middle" width="7%"> <a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjwb_sGCxBIxE3fvJN_gmrWD4auLllaRjLfXOifa6VQOgEDpOkjsnsQ819s5xnX4cWjzKug7hWLBGTlq0Lb7ARXqCB8498wwm3k4G36rY_TwWzcHX6zVNSL-5hlOJlEH7dfGgka81C4U2te/s1600/126+74_3dmap_ninja.png" imageanchor="1"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjwb_sGCxBIxE3fvJN_gmrWD4auLllaRjLfXOifa6VQOgEDpOkjsnsQ819s5xnX4cWjzKug7hWLBGTlq0Lb7ARXqCB8498wwm3k4G36rY_TwWzcHX6zVNSL-5hlOJlEH7dfGgka81C4U2te/s1600/126+74_3dmap_ninja.png" height="50" width="50" /></a></td>
<td align="center" rowspan="2" valign="middle" width="7%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj8sKD-3C31QkWzJPEriHxiHpnd77wjnQhuv0eDf3OyS82DsKDVNQRdCF5WV-PBGnPMcMDdrLQviHiYn5Fofs4mYjE3-_PTtrZeUL2Kg65b-FVpzxjHtYyUvkr8Xq8EkdAKw3y6E2R1G1rV/s1600/200_ninja3d_10dto3d.png" imageanchor="1" style="font-size: medium;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj8sKD-3C31QkWzJPEriHxiHpnd77wjnQhuv0eDf3OyS82DsKDVNQRdCF5WV-PBGnPMcMDdrLQviHiYn5Fofs4mYjE3-_PTtrZeUL2Kg65b-FVpzxjHtYyUvkr8Xq8EkdAKw3y6E2R1G1rV/s1600/200_ninja3d_10dto3d.png" height="50" width="50" /></a></td>
</tr>
<tr class="Manxcat">
<td align="center" height="20" width="6%">Full 3D Map</td>
<td align="center" height="20" valign="middle" width="4%"></td>
<td align="center" height="20" valign="middle" width="4%">--</td>
<td align="center" height="20" valign="middle" width="3%">10.04</td>
<td align="center" height="20" valign="middle" width="4%">0.0198</td>
</tr>
<tr>
<td align="center" class="table_head" rowspan="2" width="10%">9. Neighbor Joining 10D</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="6%">Internal Node Interpolation</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">9.40</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">11.42</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="3%">13.98</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">0.0285</td>
<td align="center" rowspan="2" valign="middle" width="5%">--</td>
<td align="center" rowspan="2" valign="middle" width="5%">--</td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%">n/a</td>
<td align="center" rowspan="2" valign="middle" width="6%">n/a</td>
<td align="center" class="Plots" rowspan="2" valign="middle" width="7%"><a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/mega_table_plots/200/spherical_phylogram/manxcat/200_nj_10dto3d.pviz">Spherical</a></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="7%">--</td>
<td align="center" rowspan="2" valign="middle" width="7%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgmsOWzasRzsa4g4oL1J9yLQlFVsVOovA1MoCMIvmsGYYrduu4hiWmRyweN-Op9r6Yka5iodnDC24UGQaFcsMb8_WeWJlSSdTNx5s6WNMPCyfw-UR2-rf1Uml7vNzeUNBuTjr9nPBlihopW/s1600/126%252B74_manxcat_10dto3d_sp.png" imageanchor="1" style="font-size: medium;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgmsOWzasRzsa4g4oL1J9yLQlFVsVOovA1MoCMIvmsGYYrduu4hiWmRyweN-Op9r6Yka5iodnDC24UGQaFcsMb8_WeWJlSSdTNx5s6WNMPCyfw-UR2-rf1Uml7vNzeUNBuTjr9nPBlihopW/s1600/126%252B74_manxcat_10dto3d_sp.png" height="50" width="50" /></a></td>
</tr>
<tr class="Manxcat">
<td align="center" height="20" width="6%">Full 3D Map</td>
<td align="center" height="20" valign="middle" width="4%"></td>
<td align="center" height="20" valign="middle" width="4%">--</td>
<td align="center" height="20" valign="middle" width="3%">9.9</td>
<td align="center" height="20" valign="middle" width="4%">0.0202</td>
</tr>
<tr>
<td align="center" class="table_head" rowspan="2" width="10%">10. Ninja 10D plot</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="6%">Internal Node Interpolation</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">8.65</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">12.13</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="3%">14.99</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">0.0283</td>
<td align="center" rowspan="2" valign="middle" width="5%">0.906</td>
<td align="center" rowspan="2" valign="middle" width="5%">0.834</td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%">n/a</td>
<td align="center" rowspan="2" valign="middle" width="6%">n/a</td>
<td align="center" class="Plots" rowspan="2" valign="middle" width="7%"> <a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/ninja/tree_plot/spherical_phylogram/126+74_swg_10D_plot_distance_ninja_sp.pviz">Spherical </a><br />
<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/ninja/tree_plot/cuboid_cladogram/126+74_10d_dasmacof_reroot_sideTree.pviz">Cuboid</a></td>
<td align="center" rowspan="2" valign="middle" width="6%"><a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/ninja/tree_pdf/126+74_swg_origin_10d_reroot.pdf">Rectangle</a></td>
<td align="center" rowspan="2" valign="middle" width="7%"> <a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgyf0vP24JYeFIopLTxaSMjQQxqpGVFMCjs8O44qsqYuv25js8NPxYmJadhAEhxFnQgRPs8ymqRvXT04HPA_yny3A48QZcKBra3n2-4wBoczOHjkkq-lJM06K80tQDRghDykU9dTux2F15E/s1600/126+74_10d_dasmacof_reroot_sideTree.png" imageanchor="1"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgyf0vP24JYeFIopLTxaSMjQQxqpGVFMCjs8O44qsqYuv25js8NPxYmJadhAEhxFnQgRPs8ymqRvXT04HPA_yny3A48QZcKBra3n2-4wBoczOHjkkq-lJM06K80tQDRghDykU9dTux2F15E/s1600/126+74_10d_dasmacof_reroot_sideTree.png" height="50" width="50" /></a></td>
<td align="center" rowspan="2" valign="middle" width="7%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiBMKhEPOQLN0XxrlTqecP5gMJjUMgs3DtavkcxVTQQ2r0OqACIOTupG2anVvcURCfpFyHLBytFF4kCzcjE5T_GhryXxU4EpUgtHkB5vkezvAbdMsUCTNOu__tGTY8US_nqOP-xhL8oT3l5/s1600/200_ninja10d_10dto3d.png" imageanchor="1" style="font-size: medium;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiBMKhEPOQLN0XxrlTqecP5gMJjUMgs3DtavkcxVTQQ2r0OqACIOTupG2anVvcURCfpFyHLBytFF4kCzcjE5T_GhryXxU4EpUgtHkB5vkezvAbdMsUCTNOu__tGTY8US_nqOP-xhL8oT3l5/s1600/200_ninja10d_10dto3d.png" height="50" width="50" /></a></td>
</tr>
<tr class="Manxcat">
<td align="center" height="20" width="6%">Full 3D Map</td>
<td align="center" height="20" valign="middle" width="4%"></td>
<td align="center" height="20" valign="middle" width="4%">--</td>
<td align="center" height="20" valign="middle" width="3%">10.47</td>
<td align="center" height="20" valign="middle" width="4%">0.0207</td>
</tr>
<tr>
<td align="center" class="table_head" rowspan="2" width="10%">11. Ninja Original Pid</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="6%">Internal Node Interpolation</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">9.74</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">13.03</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="3%">15.11</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">0.0273</td>
<td align="center" rowspan="2" valign="middle" width="5%">0.925</td>
<td align="center" rowspan="2" valign="middle" width="5%">0.855</td>
<td align="center" rowspan="2" valign="middle" width="6%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhl77e8rG0tr7IT6hfdRJQaw__1Lo8SDNV1ipE4dTsOlONJrZ89J9L8O4WkU56AhcmEevQLnZ1iX69qNQkAG1Pr7bHde_kUaN5-j4gA23zQ1_l0Ds2nOtgE8uYg-kMIEbzJ5xW7hZMigP3G/s1600/2.%2529whole-plot-Ninja-Edgesum-Vs-SWG-PIDDensitySat%255B0.85%255D-large_thumb%255B2%255D.png" imageanchor="1"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhl77e8rG0tr7IT6hfdRJQaw__1Lo8SDNV1ipE4dTsOlONJrZ89J9L8O4WkU56AhcmEevQLnZ1iX69qNQkAG1Pr7bHde_kUaN5-j4gA23zQ1_l0Ds2nOtgE8uYg-kMIEbzJ5xW7hZMigP3G/s1600/2.%2529whole-plot-Ninja-Edgesum-Vs-SWG-PIDDensitySat%255B0.85%255D-large_thumb%255B2%255D.png" height="50" width="50" /></a></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%">n/a</td>
<td align="center" rowspan="2" valign="middle" width="6%">n/a</td>
<td align="center" class="Plots" rowspan="2" valign="middle" width="7%"> <a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/ninja/tree_plot/spherical_phylogram/126+74_swg_origin_pid_ninja_sp.pviz">Spherical</a><br />
<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/ninja/tree_plot/cuboid_cladogram/126+74_swg_pid_dasmacof_sideTree_reroot_newcolor.pviz">Cuboid</a></td>
<td align="center" rowspan="2" valign="middle" width="6%"><a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/ninja/tree_pdf/126+74__swg_edna_pid_reroot.pdf">Rectangle</a></td>
<td align="center" rowspan="2" valign="middle" width="7%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhBFEVG5KZBfN6HyrA-I8fjEzgP_dnplCvjgc4zl0aDgLPgAQFSSaPN_njFR2VBsBVY3oZtQ44P6_ojVht_r_0t0vJW91xasCSpm6qSRrK0PWeUBpMGQywVKsjTfjmXcP-tpDvL-I-BjQCB/s1600/126+74_swg_pid_dasmacof_sideTree_reroot_newcolor.png" imageanchor="1"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhBFEVG5KZBfN6HyrA-I8fjEzgP_dnplCvjgc4zl0aDgLPgAQFSSaPN_njFR2VBsBVY3oZtQ44P6_ojVht_r_0t0vJW91xasCSpm6qSRrK0PWeUBpMGQywVKsjTfjmXcP-tpDvL-I-BjQCB/s1600/126+74_swg_pid_dasmacof_sideTree_reroot_newcolor.png" height="50" width="50" /></a> </td>
<td align="center" rowspan="2" valign="middle" width="7%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgYrO84ShE6LAVeyd1YyI2ABy6mhiAZQhOzR4D6vB17Y-FPYaDhkZ5VlfonlnxfCzMREoe1H-R7RGARbRx2H7Fr9cEpL8j6nRc3L-rWXI2a2k_m-RnpoSwF8APul2TSm4vnW2VYvYO2Voaw/s1600/200_ninja_origin_pid_10dto3d.png" imageanchor="1"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgYrO84ShE6LAVeyd1YyI2ABy6mhiAZQhOzR4D6vB17Y-FPYaDhkZ5VlfonlnxfCzMREoe1H-R7RGARbRx2H7Fr9cEpL8j6nRc3L-rWXI2a2k_m-RnpoSwF8APul2TSm4vnW2VYvYO2Voaw/s1600/200_ninja_origin_pid_10dto3d.png" height="50" width="50" /></a></td>
</tr>
<tr class="Manxcat">
<td align="center" height="20" width="6%"><div class="separator" style="clear: both; text-align: center;">
<br /></div>
Full 3D Map</td>
<td align="center" height="20" valign="middle" width="4%"></td>
<td align="center" height="20" valign="middle" width="4%">--</td>
<td align="center" height="20" valign="middle" width="3%">11.67</td>
<td align="center" height="20" valign="middle" width="4%">0.0203</td>
</tr>
<tr><td class="noborder" height="1" width="8%"></td></tr>
<tr>
<th class="table_head" rowspan="22" scope="row" width="8%">126 + 74 + 988 + 945 (2133) sequences<br />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgQs2trltGn2NA-1uXaRK91c-bJjZGXV58-rsfqesoSb6SHvHzn_EH7jX0eVouAup9VIy-YXU8j-d_BlmvLnbRGkaZVFwcFxiJo2uAG2drBfYqTCrpHTR8acM0Beg2Je2nzLgvT-M4Qvwpn/s1600/2133_edgeSum.PNG">Edge Sum Comparison Figure</a></th>
<td align="center" class="table_head" rowspan="2" width="10%">A. Clustal Omega 1 iter Raxml</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="6%">Internal Node Interpolation</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">67.95</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">91.31</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="3%">99.9</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">0.025</td>
<td align="center" rowspan="2" valign="middle" width="5%">0.138</td>
<td align="center" rowspan="2" valign="middle" width="5%">0.145</td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"><div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhgDlr_jcGqKgnSPvM94qJt4qeiMPdhZadVRpZHWozR2N-E2iUmgMidARfTm4U9LPNQZQjk18IMT7uRk4bSLD-2fFYau6uCeA_s1wx7t8a2H_RurWnEfqw-xNL9QrDU0nLqzykhUqJkrDc/s1600/whole-plot-ClustalOStrictPIDNG-Vs-SWGPIDDensitySat%255B0.85%255D-large.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhgDlr_jcGqKgnSPvM94qJt4qeiMPdhZadVRpZHWozR2N-E2iUmgMidARfTm4U9LPNQZQjk18IMT7uRk4bSLD-2fFYau6uCeA_s1wx7t8a2H_RurWnEfqw-xNL9QrDU0nLqzykhUqJkrDc/s200/whole-plot-ClustalOStrictPIDNG-Vs-SWGPIDDensitySat%255B0.85%255D-large.png" height="50" width="40" /></a></div>
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<td align="left" rowspan="2" valign="middle" width="6%"><div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgQI9uDO5OYcDvDW-gehTkaf-fR4SRK8DcWNaNiRTLXDteQqmni3sauu7PPkt-CqxmoLnTr92A5y4La-6xW7ciDh0MgEdSTEzNa3k9DH6GJx3p8t8Er8PMIV_2DCmqHLO6zAhovBzWL5EA/s1600/whole-plot-ClustalOFullPIDNG-Vs-SWGPIDDensitySat%255B0.85%255D-large.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgQI9uDO5OYcDvDW-gehTkaf-fR4SRK8DcWNaNiRTLXDteQqmni3sauu7PPkt-CqxmoLnTr92A5y4La-6xW7ciDh0MgEdSTEzNa3k9DH6GJx3p8t8Er8PMIV_2DCmqHLO6zAhovBzWL5EA/s200/whole-plot-ClustalOFullPIDNG-Vs-SWGPIDDensitySat%255B0.85%255D-large.png" height="50" width="40" /></a></div>
</td>
<td align="center" class="Plots" rowspan="2" valign="middle" width="7%"><a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/qiime/tree_plot/spherical_phylogram/2133_clustalO_aligned_raxml_sp.pviz">Spherical </a><br />
<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/qiime/tree_plot/rectangular_cladogram/2133_clustalO_aligned_raxml_sideTree.pviz">Cuboid</a></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="7%"><div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhLDdOTrE1hLD7JbhENEnJSuezfQZRJrUhp7rZgB_XEoaqz1a5z-1dqaO2ESqMEJcqD79mVrXzaqgqxXSCdcdaSP-Z9eSR3BbcHADMKZNXOvNgRWBmxRXrIKVB8rcu-iSsOmToj9DDJOZhg/s1600/2133_clustalO_aligned_raxml_sideTree.png" imageanchor="1"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhLDdOTrE1hLD7JbhENEnJSuezfQZRJrUhp7rZgB_XEoaqz1a5z-1dqaO2ESqMEJcqD79mVrXzaqgqxXSCdcdaSP-Z9eSR3BbcHADMKZNXOvNgRWBmxRXrIKVB8rcu-iSsOmToj9DDJOZhg/s1600/2133_clustalO_aligned_raxml_sideTree.png" height="50" width="50" /></a></div>
<br /></td>
<td align="center" rowspan="2" valign="middle" width="7%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiArzvjOwZ3bKVftLMBe-53beOZg_n6wa8PFHEBm9XgbfqqxPkdw4d6H0Jz_B-4EftvtJ8SOyC5vW1eTluICwPvQnFG_bfK46yQc9Zs2TsIJ9Ie73_7xMVNOTUNzdyPa9Uv6NXtxlujo8YN/s1600/2133_clustalO_aligned_raxml_sp.png" imageanchor="1"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiArzvjOwZ3bKVftLMBe-53beOZg_n6wa8PFHEBm9XgbfqqxPkdw4d6H0Jz_B-4EftvtJ8SOyC5vW1eTluICwPvQnFG_bfK46yQc9Zs2TsIJ9Ie73_7xMVNOTUNzdyPa9Uv6NXtxlujo8YN/s1600/2133_clustalO_aligned_raxml_sp.png" height="50" width="50" /></a></td>
</tr>
<tr class="Manxcat">
<td align="center" height="20" width="6%">Full 3D Map</td>
<td align="center" height="20" valign="middle" width="4%"></td>
<td align="center" height="20" valign="middle" width="4%">--</td>
<td align="center" height="20" valign="middle" width="3%">90.76</td>
<td align="center" height="20" valign="middle" width="4%">0.0229</td>
</tr>
<tr>
<td align="center" class="table_head" rowspan="2" width="10%">B. Clustal Omega 1 iter FastTree</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="6%">Internal Node Interpolation</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">71.11</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%"><br /></td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="3%">104.65</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%"></td>
<td align="center" rowspan="2" valign="middle" width="5%">--</td>
<td align="center" rowspan="2" valign="middle" width="5%">--</td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%">Same as A</td>
<td align="center" rowspan="2" valign="middle" width="6%">Same as A</td>
<td align="center" class="Plots" rowspan="2" valign="middle" width="7%"><a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/mega_table_plots/2133/spherical_phylogram/2133_clustalO_aligned_fastTree_sp.pviz">Spherical</a><br />
<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/mega_table_plots/2133/cuboid_cladogram/2133_clustalO_aligned_fastTree_sideTree.pviz">Cuboid</a></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="7%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjr4luiiWHep31UFl60CWv2glQLup4EirjHI6vxhkDrj5w6vYDI-C4iR1GO2vn_b1A0drvaEuUAkUnsIin_jDDBavkmLjwjJSoIfXEIkn4chptOWd_4ZhAa7rakmc6NuKzLRt1c3Mp4gSAM/s1600/2133_clustalO_aligned_fastTree_sideTree.png" imageanchor="1"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjr4luiiWHep31UFl60CWv2glQLup4EirjHI6vxhkDrj5w6vYDI-C4iR1GO2vn_b1A0drvaEuUAkUnsIin_jDDBavkmLjwjJSoIfXEIkn4chptOWd_4ZhAa7rakmc6NuKzLRt1c3Mp4gSAM/s1600/2133_clustalO_aligned_fastTree_sideTree.png" height="50" width="50" /></a></td>
<td align="center" rowspan="2" valign="middle" width="7%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjKcKteBdQ0e-Xg-Vw6JkGO79waxXtNS3iAAeYuxOtUAfgt5Powvw-d07mceyIPoA9kBAVRsOtrqR0IrDvOX7PIU29qCwnMNhTmCYEMnhvTfe1-FhwZa2XEQo5Dlic0PlipY3J8vgzrgIhk/s1600/2133_clustalO_aligned_fastTree_sp.png" imageanchor="1"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjKcKteBdQ0e-Xg-Vw6JkGO79waxXtNS3iAAeYuxOtUAfgt5Powvw-d07mceyIPoA9kBAVRsOtrqR0IrDvOX7PIU29qCwnMNhTmCYEMnhvTfe1-FhwZa2XEQo5Dlic0PlipY3J8vgzrgIhk/s1600/2133_clustalO_aligned_fastTree_sp.png" height="50" width="50" /></a></td>
</tr>
<tr class="Manxcat">
<td align="center" height="20" width="6%">Full 3D Map</td>
<td align="center" height="20" valign="middle" width="4%"></td>
<td align="center" height="20" valign="middle" width="4%">--</td>
<td align="center" height="20" valign="middle" width="3%"></td>
<td align="center" height="20" valign="middle" width="4%"></td>
</tr>
<tr>
<td align="center" class="table_head" rowspan="2" width="10%">C. Clustal Omega Anna Raxml</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="6%">Internal Node Interpolation</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">68.34</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">93.91</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="3%">102.23</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">0.025</td>
<td align="center" rowspan="2" valign="middle" width="5%">0.679</td>
<td align="center" rowspan="2" valign="middle" width="5%">0.714</td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" class="Plots" rowspan="2" valign="middle" width="7%"> <a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/qiime/tree_plot/spherical_phylogram/2133_clustalO_anna_aligned_raxml_sp.pviz">Spherical </a><br />
<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/qiime/tree_plot/rectangular_cladogram/2133_clustalO_anna_aligned_raxml_sideTree.pviz">Cuboid</a></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="7%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhthNCfv8Id5A2ipGzi2-ClNu2T0hWv__-WBopphDGWLjRcI1e4_a_Kxtw0GZCT-5UpjaMDAoqLlyqZTRGnU1_IYHkSGW1MKqYeO1MtYSeJ2zThnWVsOkyhiJ_2SoeK5GG9R91NOspCYVjL/s1600/2133_clustalO_anna_aligned_raxml_sideTree.png" imageanchor="1"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhthNCfv8Id5A2ipGzi2-ClNu2T0hWv__-WBopphDGWLjRcI1e4_a_Kxtw0GZCT-5UpjaMDAoqLlyqZTRGnU1_IYHkSGW1MKqYeO1MtYSeJ2zThnWVsOkyhiJ_2SoeK5GG9R91NOspCYVjL/s1600/2133_clustalO_anna_aligned_raxml_sideTree.png" height="50" width="50" /></a></td>
<td align="center" rowspan="2" valign="middle" width="7%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi6NUJPoOwDbh46b00z6XluV8MtIEBfYZJZU6v2sN2dQDVPJ7EoJlVc9qWWa9y0SgeI-sTSyq4RvGXAa5aMZrvSNPWcimyjzY09tnI3ml1dkvQauzGg32Aujg2smPJvhh2-v_WcgyssGy_6/s1600/2131_clustalO_anna_aligned_raxml_sp.png" imageanchor="1"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi6NUJPoOwDbh46b00z6XluV8MtIEBfYZJZU6v2sN2dQDVPJ7EoJlVc9qWWa9y0SgeI-sTSyq4RvGXAa5aMZrvSNPWcimyjzY09tnI3ml1dkvQauzGg32Aujg2smPJvhh2-v_WcgyssGy_6/s1600/2131_clustalO_anna_aligned_raxml_sp.png" height="50" width="50" /></a></td>
</tr>
<tr class="Manxcat">
<td align="center" height="20" width="6%">Full 3D Map</td>
<td align="center" height="20" valign="middle" width="4%"></td>
<td align="center" height="20" valign="middle" width="4%">--</td>
<td align="center" height="20" valign="middle" width="3%">93.18</td>
<td align="center" height="20" valign="middle" width="4%">0.0226</td>
</tr>
<tr>
<td align="center" class="table_head" rowspan="2" width="10%">D. Clustal Omega 10 iter Raxml</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="6%">Internal Node Interpolation</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">63.51</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">82.1</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="3%">96.95</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">0.0262</td>
<td align="center" rowspan="2" valign="middle" width="5%">0.272</td>
<td align="center" rowspan="2" valign="middle" width="5%">0.284</td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"><div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhx896HeeLnfZUrHKpxFYY3_3Mppf2zYgDh_rGlSlb5yh6NUaSn76OMo5VY4U2yjCmT66OEBEpldZ2cKMXeKcA07e7dW6iTalQQUn4giMz53bCg3-lRcuMAPwKV3nBVkrj3z7AUqPgHiNw/s1600/whole-plot-ClustalO10iterStrictPIDNG-Vs-SWGPIDDensitySat%255B0.85%255D-large.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhx896HeeLnfZUrHKpxFYY3_3Mppf2zYgDh_rGlSlb5yh6NUaSn76OMo5VY4U2yjCmT66OEBEpldZ2cKMXeKcA07e7dW6iTalQQUn4giMz53bCg3-lRcuMAPwKV3nBVkrj3z7AUqPgHiNw/s200/whole-plot-ClustalO10iterStrictPIDNG-Vs-SWGPIDDensitySat%255B0.85%255D-large.png" height="50" width="40" /></a></div>
</td>
<td align="left" rowspan="2" valign="middle" width="6%"><div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjtnkMCd2TwRrYRNQvGUYdczDtEFbvBonljZORtL54ACOd-6KTztA_BUXCdJSaQbGNfWYNsJ7otA02p-JJUczaDQ9yBFtTXVkZ9irDkT1NQpkFdlZsZd2jzwkXfSghYJUA_ylqX9p3nrwk/s1600/whole-plot-ClustalO10iterFullPIDNG-Vs-SWGPIDDensitySat%255B0.85%255D-large.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjtnkMCd2TwRrYRNQvGUYdczDtEFbvBonljZORtL54ACOd-6KTztA_BUXCdJSaQbGNfWYNsJ7otA02p-JJUczaDQ9yBFtTXVkZ9irDkT1NQpkFdlZsZd2jzwkXfSghYJUA_ylqX9p3nrwk/s200/whole-plot-ClustalO10iterFullPIDNG-Vs-SWGPIDDensitySat%255B0.85%255D-large.png" height="50" width="40" /></a></div>
</td>
<td align="center" class="Plots" rowspan="2" valign="middle" width="7%"><a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/qiime/tree_plot/spherical_phylogram/2133_clustalO_aligned_10iter_raxml_sp.pviz">Spherical </a><br />
<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/qiime/tree_plot/rectangular_cladogram/2131_clustalO_aligned_iter10_raxml_sideTree.pviz">Cuboid</a></td>
<td align="center" rowspan="2" valign="middle" width="6%"><a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/qiime/tree_pdf/2131_clustalO_10_iter_raxml_reroot_colored.pdf">Rectangle</a></td>
<td align="center" rowspan="2" valign="middle" width="7%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiJEh9EFv75h2LJUW3rVgwvanNmpkt6D559spCOxm7-s8qqqkHe6p1HfKPS_9kDMGieOnqUL5oLrkckkj7GGrJRRgdO6pCQEbaok0ye4RNVEQ193gh_tBp8d0BjHbF7cJcALqO5aALOt479/s1600/2131_clustalO_aligned_iter10_raxml_sideTree_1.png" imageanchor="1"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiJEh9EFv75h2LJUW3rVgwvanNmpkt6D559spCOxm7-s8qqqkHe6p1HfKPS_9kDMGieOnqUL5oLrkckkj7GGrJRRgdO6pCQEbaok0ye4RNVEQ193gh_tBp8d0BjHbF7cJcALqO5aALOt479/s1600/2131_clustalO_aligned_iter10_raxml_sideTree_1.png" height="50" width="50" /></a></td>
<td align="center" rowspan="2" valign="middle" width="7%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhWPhme8XZ8PQIiD-zQLCAH6J6I4Ob5hYrcPdnrWq157-lGjjYL4APy-38RUbU3b3B_gh0fsQMlVSeG9v0QNrMTFkxO2CCAq1g_vnIQ442vvLIDpf9-XpLTOJsxCbfauTo_L7LkDaYfxeeu/s1600/2131_clustalO_aligned_10iter_raxml_sp.png" imageanchor="1"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhWPhme8XZ8PQIiD-zQLCAH6J6I4Ob5hYrcPdnrWq157-lGjjYL4APy-38RUbU3b3B_gh0fsQMlVSeG9v0QNrMTFkxO2CCAq1g_vnIQ442vvLIDpf9-XpLTOJsxCbfauTo_L7LkDaYfxeeu/s1600/2131_clustalO_aligned_10iter_raxml_sp.png" height="50" width="50" /></a></td>
</tr>
<tr class="Manxcat">
<td align="center" height="20" width="6%">Full 3D Map</td>
<td align="center" height="20" valign="middle" width="4%"></td>
<td align="center" height="20" valign="middle" width="4%">--</td>
<td align="center" height="20" valign="middle" width="3%">82.25</td>
<td align="center" height="20" valign="middle" width="4%">0.0232</td>
</tr>
<tr>
<td align="center" class="table_head" rowspan="2" width="10%">E. Clustal Omega 20 iter Raxml</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="6%">Internal Node Interpolation</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">58.84</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">81.09</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="3%">93.64</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">0.0252</td>
<td align="center" rowspan="2" valign="middle" width="5%">0.275</td>
<td align="center" rowspan="2" valign="middle" width="5%">0.288</td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"><div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh-fHMrklNj1RNSaI1xlO3td2jtU5JYCbCRiSFZysJZZZgxhqV6lhZJkEmq-VMX9nyw0kmajmvXtyWbfM24oSH22UTu0IB1rioMG5SXjV-pzRrNfNKitmW0XPQiOoRUczopUqXhREUf2Mo/s1600/whole-plot-ClustalO20iterStrictPIDNG-Vs-SWGPIDDensitySat%255B0.85%255D-large.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh-fHMrklNj1RNSaI1xlO3td2jtU5JYCbCRiSFZysJZZZgxhqV6lhZJkEmq-VMX9nyw0kmajmvXtyWbfM24oSH22UTu0IB1rioMG5SXjV-pzRrNfNKitmW0XPQiOoRUczopUqXhREUf2Mo/s200/whole-plot-ClustalO20iterStrictPIDNG-Vs-SWGPIDDensitySat%255B0.85%255D-large.png" height="50" width="40" /></a></div>
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<td align="left" rowspan="2" valign="middle" width="6%"><div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj3tRbTKLhxfzC_YSAFt8mPyGYIvlS9em6W7qapG5GppA3oGwynK217d60qJ05TH21qKsP4Rtpu2dXKLIbeiNyl9kYXhPLcAJQod7QTSwn99w0atXguiHfyYSVplomLz5eJ_lKCn9ucEHQ/s1600/whole-plot-ClustalO20iterFullPIDNG-Vs-SWGPIDDensitySat%255B0.85%255D-large.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj3tRbTKLhxfzC_YSAFt8mPyGYIvlS9em6W7qapG5GppA3oGwynK217d60qJ05TH21qKsP4Rtpu2dXKLIbeiNyl9kYXhPLcAJQod7QTSwn99w0atXguiHfyYSVplomLz5eJ_lKCn9ucEHQ/s200/whole-plot-ClustalO20iterFullPIDNG-Vs-SWGPIDDensitySat%255B0.85%255D-large.png" height="50" width="40" /></a></div>
</td>
<td align="center" class="Plots" rowspan="2" valign="middle" width="7%"><a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/qiime/tree_plot/spherical_phylogram/2133_clustalO_aligned_20iter_raxml_sp.pviz">Spherical </a><br />
<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/qiime/tree_plot/rectangular_cladogram/2133_clustalO_aligned_20iter_raxml_sideTree.pviz">Cuboid</a></td>
<td align="center" rowspan="2" valign="middle" width="6%"><a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/qiime/tree_pdf/2131_clustalO_20_iter_raxml_reroot_colored.pdf">Rectangle</a></td>
<td align="center" rowspan="2" valign="middle" width="7%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjh4KsCdcZOlai4pTOLdua8-1FzWjvRdP3eUgf_GI_JKmCUeX3_QKJP1D1M1I9wT6gS49Pc1ovBhacKRWeENDlnAqYS3OZTywdIAGKE7ksGi-a-2-hKOjqtjrg8Vwm3eUhqMuDg5n201i9j/s1600/2133_clustalO_aligned_20iter_raxml_sideTree.png" imageanchor="1"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjh4KsCdcZOlai4pTOLdua8-1FzWjvRdP3eUgf_GI_JKmCUeX3_QKJP1D1M1I9wT6gS49Pc1ovBhacKRWeENDlnAqYS3OZTywdIAGKE7ksGi-a-2-hKOjqtjrg8Vwm3eUhqMuDg5n201i9j/s1600/2133_clustalO_aligned_20iter_raxml_sideTree.png" height="50" width="50" /></a></td>
<td align="center" rowspan="2" valign="middle" width="7%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh0GBLZpu-mK2Tu7VYErNvh47snF7w6v4bvaKiW0Voij6DJTLP9fZAuHtlTCEx9AGwKyjEhCDn-AJBLkiowOJAlZ5dfxRK_ecJbfZ72AloQmhmVcKgc7GGwCpYSPv6BDfP10SHkLnTg_EJa/s1600/2131_clustalO_aligned_20iter_raxml_sp.png" imageanchor="1"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh0GBLZpu-mK2Tu7VYErNvh47snF7w6v4bvaKiW0Voij6DJTLP9fZAuHtlTCEx9AGwKyjEhCDn-AJBLkiowOJAlZ5dfxRK_ecJbfZ72AloQmhmVcKgc7GGwCpYSPv6BDfP10SHkLnTg_EJa/s1600/2131_clustalO_aligned_20iter_raxml_sp.png" height="50" width="50" /></a></td>
</tr>
<tr class="Manxcat">
<td align="center" height="20" width="6%">Full 3D Map</td>
<td align="center" height="20" valign="middle" width="4%"></td>
<td align="center" height="20" valign="middle" width="4%">--</td>
<td align="center" height="20" valign="middle" width="3%">80.88</td>
<td align="center" height="20" valign="middle" width="4%">0.0229</td>
</tr>
<tr>
<td align="center" class="table_head" rowspan="2" width="10%">F. Muscle 2 iter Raxml</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="6%">Internal Node Interpolation</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">84.23</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">105.52</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="3%">113.82</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">0.0255</td>
<td align="center" rowspan="2" valign="middle" width="5%">0.422</td>
<td align="center" rowspan="2" valign="middle" width="5%">0.451</td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"><div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgQicFbVFQ_Q5xm-LJqAGvXzT2kpatRllQ43eggk7ozIsua2HvR3xepfN6eUg6c7kdDEm5uvRyA0TM1LWnAkGNFIU3x8agB4NcpXOG3t3no96lRxxcGjWMYr1nxtLeCVO5-VUnRafTn9ik/s1600/whole-plot-MuscleStrictPIDNG-Vs-SWGPIDDensitySat%255B0.85%255D-large.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgQicFbVFQ_Q5xm-LJqAGvXzT2kpatRllQ43eggk7ozIsua2HvR3xepfN6eUg6c7kdDEm5uvRyA0TM1LWnAkGNFIU3x8agB4NcpXOG3t3no96lRxxcGjWMYr1nxtLeCVO5-VUnRafTn9ik/s200/whole-plot-MuscleStrictPIDNG-Vs-SWGPIDDensitySat%255B0.85%255D-large.png" height="50" width="40" /></a></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjnIIx658ol-lCQ_VuOEYEDTrC9AbfjalSw0eLQfIKm7wjrZn6u-LsYsDikzwoN8d-ooErOMQLgVVahrtgr17RpUdrhyqpqXCD3oBflDpeed8HglpaOoXmYvcGDkEXqURhLXtsLx-J9EM4/s1600/whole-plot-MuscleFullPIDNG-Vs-SWGPIDDensitySat%255B0.85%255D-large.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjnIIx658ol-lCQ_VuOEYEDTrC9AbfjalSw0eLQfIKm7wjrZn6u-LsYsDikzwoN8d-ooErOMQLgVVahrtgr17RpUdrhyqpqXCD3oBflDpeed8HglpaOoXmYvcGDkEXqURhLXtsLx-J9EM4/s200/whole-plot-MuscleFullPIDNG-Vs-SWGPIDDensitySat%255B0.85%255D-large.png" height="50" width="40" /></a></div>
</td>
<td align="center" class="Plots" rowspan="2" valign="middle" width="7%"><a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/qiime/tree_plot/spherical_phylogram/2133_muscle_aligned_raxml_sp.pviz">Spherical </a><br />
<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/qiime/tree_plot/rectangular_cladogram/2133_muscle_aligned_sideTree_reroot_newColor.pviz">Cuboid</a></td>
<td align="center" rowspan="2" valign="middle" width="6%"><a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/qiime/tree_pdf/2133_muscle_aligned_reroot.pdf">Rectangle</a></td>
<td align="center" rowspan="2" valign="middle" width="7%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjn6ECjvgpSVsWM8pCER5viMsDlr7808PVXvUW0MCz8sqimhK0tOmNj-6CE56ICIiY_piUlrYeRNlySTqubsWnEGvnhwNhW6PSYTqIKuAZMAXfJ0em29nBZ7b2FKWrjxu2PAFepNSDS3Pa9/s1600/2133_muscle_aligned_sideTree.png" imageanchor="1"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjn6ECjvgpSVsWM8pCER5viMsDlr7808PVXvUW0MCz8sqimhK0tOmNj-6CE56ICIiY_piUlrYeRNlySTqubsWnEGvnhwNhW6PSYTqIKuAZMAXfJ0em29nBZ7b2FKWrjxu2PAFepNSDS3Pa9/s1600/2133_muscle_aligned_sideTree.png" height="50" width="50" /></a></td>
<td align="center" rowspan="2" valign="middle" width="7%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiKD8NTOG4g6jIA4Oyfj7xCfm-oPT_ryTQmCKbhNthRIMKjJq17Od5nm-nKR65w7GgVvM_HTKrL78bEFD-eRhWYKhT8LOHec8RbZz5oFurrvbx-OR6wTqWxMJH5iYJwD-2H8LgXOWbLLJ6o/s1600/2133_muscle_aligned_raxml_sp.png" imageanchor="1"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiKD8NTOG4g6jIA4Oyfj7xCfm-oPT_ryTQmCKbhNthRIMKjJq17Od5nm-nKR65w7GgVvM_HTKrL78bEFD-eRhWYKhT8LOHec8RbZz5oFurrvbx-OR6wTqWxMJH5iYJwD-2H8LgXOWbLLJ6o/s1600/2133_muscle_aligned_raxml_sp.png" height="50" width="50" /></a></td>
</tr>
<tr class="Manxcat">
<td align="center" height="20" width="6%">Full 3D Map</td>
<td align="center" height="20" valign="middle" width="4%"></td>
<td align="center" height="20" valign="middle" width="4%">--</td>
<td align="center" height="20" valign="middle" width="3%">103.03</td>
<td align="center" height="20" valign="middle" width="4%">0.0229</td>
</tr>
<tr>
<td align="center" class="table_head" rowspan="2" width="10%">G. Neighbor Joining 3D</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="6%">Internal Node Interpolation</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">26.59</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">71.89</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="3%">--</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">--</td>
<td align="center" rowspan="2" valign="middle" width="5%">--</td>
<td align="center" rowspan="2" valign="middle" width="5%">--</td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%">n/a</td>
<td align="center" rowspan="2" valign="middle" width="6%">n/a</td>
<td align="center" class="Plots" rowspan="2" valign="middle" width="7%"><a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/nj/tree_plot/spherical_phylogram/2133_swg_pid_nj_sp.pviz">Spherical</a></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="7%">--</td>
<td align="center" rowspan="2" valign="middle" width="7%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiw4YyiNP3BpxcrYVpD7s7mvlBs9J8gxXpGL2tJ_FqeGpWZ0PAfl142VO8o8SmV9Pw7pmFZKJvg0KaiAyvdOPOif9q4npwRG3Hjk2CQNaljxnHrEinGqiaHWCTNwIZFS0gi0vUzS3ilETuv/s1600/2133_swg_pid_nj_sp.png" imageanchor="1"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiw4YyiNP3BpxcrYVpD7s7mvlBs9J8gxXpGL2tJ_FqeGpWZ0PAfl142VO8o8SmV9Pw7pmFZKJvg0KaiAyvdOPOif9q4npwRG3Hjk2CQNaljxnHrEinGqiaHWCTNwIZFS0gi0vUzS3ilETuv/s1600/2133_swg_pid_nj_sp.png" height="50" width="50" /></a></td>
</tr>
<tr class="Manxcat">
<td align="center" height="20" width="6%">Full 3D Map</td>
<td align="center" height="20" valign="middle" width="4%"></td>
<td align="center" height="20" valign="middle" width="4%">--</td>
<td align="center" height="20" valign="middle" width="3%">--</td>
<td align="center" height="20" valign="middle" width="4%">--</td>
</tr>
<tr>
<td align="center" class="table_head" rowspan="2" width="10%">H. Ninja 3D plot</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="6%">Internal Node Interpolation</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">27.59</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">72.12</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="3%">86.45</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">0.0268</td>
<td align="center" rowspan="2" valign="middle" width="5%">0.519</td>
<td align="center" rowspan="2" valign="middle" width="5%">0.575</td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%">n/a</td>
<td align="center" rowspan="2" valign="middle" width="6%">n/a</td>
<td align="center" class="Plots" rowspan="2" valign="middle" width="7%"><a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/ninja/tree_plot/spherical_phylogram/2133_ninja_pid_3D_plot_distance_sp.pviz">Spherical</a><br />
<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/ninja/tree_plot/rectangular_cladogram/2133_swg_pid_dasmacof_grouped_3d_dist_sideTree.pviz">Cuboid</a></td>
<td align="center" rowspan="2" valign="middle" width="6%"><a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/ninja/tree_pdf/2133_swg_pid_dasmacof_grouped_3d_dist_reroot_colored.pdf">Rectangle</a></td>
<td align="center" rowspan="2" valign="middle" width="7%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh883d03bU8qVkN7giVTPHg0xPNALzpHNDtbH_WS67f6npibVYTX-3-Mo8YdPp1_Q0ODLmCwGLAPVWij9NLFC4ByS6wk1RbajqHg3_kk5dI4u_cIC-1A0tWKfoxzJdKRGOlUKZ4ja4swejw/s1600/2133_ninja_3d_dist_sideTree.png" imageanchor="1"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh883d03bU8qVkN7giVTPHg0xPNALzpHNDtbH_WS67f6npibVYTX-3-Mo8YdPp1_Q0ODLmCwGLAPVWij9NLFC4ByS6wk1RbajqHg3_kk5dI4u_cIC-1A0tWKfoxzJdKRGOlUKZ4ja4swejw/s1600/2133_ninja_3d_dist_sideTree.png" height="50" width="50" /></a></td>
<td align="center" rowspan="2" valign="middle" width="7%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEglMqmkc0Frzff0kktn7VLNxQIjllEE2d2t-1nF5QEWBKZOwQZcYx_TX4IJaOVRae6Me-X8x4I47m-8Dm_IqnNOjAgREVHu0YrnukjWAPE3HeK6G7Dgf122pJI3m1owwwWKVWtn2_MXF7y2/s1600/2133_ninja_pid_3D_plot_distance_sp.png" imageanchor="1"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEglMqmkc0Frzff0kktn7VLNxQIjllEE2d2t-1nF5QEWBKZOwQZcYx_TX4IJaOVRae6Me-X8x4I47m-8Dm_IqnNOjAgREVHu0YrnukjWAPE3HeK6G7Dgf122pJI3m1owwwWKVWtn2_MXF7y2/s1600/2133_ninja_pid_3D_plot_distance_sp.png" height="50" width="50" /></a></td>
</tr>
<tr class="Manxcat">
<td align="center" height="20" width="6%">Full 3D Map</td>
<td align="center" height="20" valign="middle" width="4%"></td>
<td align="center" height="20" valign="middle" width="4%">--</td>
<td align="center" height="20" valign="middle" width="3%">66.61</td>
<td align="center" height="20" valign="middle" width="4%">0.023</td>
</tr>
<tr>
<td align="center" class="table_head" rowspan="2" width="10%">I. Neighbor Joining 10D</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="6%">Internal Node Interpolation</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">39.85</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">52.56</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="3%">81.68</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">0.028</td>
<td align="center" rowspan="2" valign="middle" width="5%">--</td>
<td align="center" rowspan="2" valign="middle" width="5%">--</td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhi7bRwrItbndVemRwOkJhexple_VHkf8n61w0dK5Er9zT19JlSgCj0o_l5g9900zZhfb0kY54AwWDd3RA9RWjyiFR1boqAjGtAxSuuUagozjNt3PNeNdvMUkcRWumPy_9Oeq7-0NEqLThX/s1600/whole-plot-10d.to.3d.nj-Vs-10d.to.3d.manxcatDensitySat%255B0.85%255D-large.png" imageanchor="1"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhi7bRwrItbndVemRwOkJhexple_VHkf8n61w0dK5Er9zT19JlSgCj0o_l5g9900zZhfb0kY54AwWDd3RA9RWjyiFR1boqAjGtAxSuuUagozjNt3PNeNdvMUkcRWumPy_9Oeq7-0NEqLThX/s1600/whole-plot-10d.to.3d.nj-Vs-10d.to.3d.manxcatDensitySat%255B0.85%255D-large.png" height="50" width="40" /></a></td>
<td align="center" rowspan="2" valign="middle" width="6%">n/a</td>
<td align="center" rowspan="2" valign="middle" width="6%">n/a</td>
<td align="center" class="Plots" rowspan="2" valign="middle" width="7%"><a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/mega_table_plots/2133/spherical_phylogram/2133_manxcat_10dto3d_nj_sp.pviz">Spherical</a></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="7%">--</td>
<td align="center" rowspan="2" valign="middle" width="7%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiFV7JzYtlcWY4wjDjN2c8HePp8pZtJ_b5xzWQuQKtr1k5bFLjUeL5JvBGkBeWuIEMPfiNiIzbhVyFbBKCZ-AZqhvghBoxwgURCdHd_uJ-u_Sf0_iSjIBTF3XeXEY_-pJtjFewwqcyzxmbd/s1600/2133_manxcat_10dto3d_nj_sp.png" imageanchor="1"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiFV7JzYtlcWY4wjDjN2c8HePp8pZtJ_b5xzWQuQKtr1k5bFLjUeL5JvBGkBeWuIEMPfiNiIzbhVyFbBKCZ-AZqhvghBoxwgURCdHd_uJ-u_Sf0_iSjIBTF3XeXEY_-pJtjFewwqcyzxmbd/s1600/2133_manxcat_10dto3d_nj_sp.png" height="50" width="50" /></a></td>
</tr>
<tr class="Manxcat">
<td align="center" height="20" width="6%">Full 3D Map</td>
<td align="center" height="20" valign="middle" width="4%"></td>
<td align="center" height="20" valign="middle" width="4%">--</td>
<td align="center" height="20" valign="middle" width="3%">61.16</td>
<td align="center" height="20" valign="middle" width="4%">0.0233</td>
</tr>
<tr>
<td align="center" class="table_head" rowspan="2" width="10%">J. Ninja 10D transform</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="6%">Internal Node Interpolation</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">40.33</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">58.52</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="3%">82.23</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">0.0264</td>
<td align="center" rowspan="2" valign="middle" width="5%">0.728</td>
<td align="center" rowspan="2" valign="middle" width="5%">0.781</td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%">n/a</td>
<td align="center" rowspan="2" valign="middle" width="6%">n/a</td>
<td align="center" class="Plots" rowspan="2" valign="middle" width="7%"><a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/ninja/tree_plot/spherical_phylogram/2133_ninja_pid_10d_distance_sp.pviz">Spherical</a><br />
<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/ninja/tree_plot/rectangular_cladogram/2133_10d_dist_reroot_ninja_sideTree.pviz">Cuboid</a></td>
<td align="center" rowspan="2" valign="middle" width="6%"><a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/ninja/tree_pdf/dasmacof.2133.10d.ninja.reroot.pdf">Rectangle</a></td>
<td align="center" rowspan="2" valign="middle" width="7%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiAYak7_X7vCmxAE47XUu2jOYu4wGrAsjzEh4J8VBXFgrcN8hH8NNSAX0yrNKW-iK5PTgFJSzTGlayQN6OS8u5_eGUaWWdhZGqd1ZyVcMmDOFfAI7ZmvVb8Ekpv1bQ9uou1W8APBGP8-xgU/s1600/2133_10d_dist_reroot_ninja_sideTree.png" imageanchor="1"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiAYak7_X7vCmxAE47XUu2jOYu4wGrAsjzEh4J8VBXFgrcN8hH8NNSAX0yrNKW-iK5PTgFJSzTGlayQN6OS8u5_eGUaWWdhZGqd1ZyVcMmDOFfAI7ZmvVb8Ekpv1bQ9uou1W8APBGP8-xgU/s1600/2133_10d_dist_reroot_ninja_sideTree.png" height="50" width="50" /></a></td>
<td align="center" rowspan="2" valign="middle" width="7%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhXWwpTHdK1LITqUtjyLmEKAxqO4DwRE0cR_zs_cuiE9BoJ9VBLLbA5hMMpOdF8ktlNLbeW7s2EXCdxlrdkCBpP5qBCWh-BT8xRZeovk8_X6zgihf_PagTtc57OilJ43FtS1pBcRaI4ysIC/s1600/2133_ninja_pid_10d_distance_sp.png" imageanchor="1"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhXWwpTHdK1LITqUtjyLmEKAxqO4DwRE0cR_zs_cuiE9BoJ9VBLLbA5hMMpOdF8ktlNLbeW7s2EXCdxlrdkCBpP5qBCWh-BT8xRZeovk8_X6zgihf_PagTtc57OilJ43FtS1pBcRaI4ysIC/s1600/2133_ninja_pid_10d_distance_sp.png" height="50" width="50" /></a></td>
</tr>
<tr class="Manxcat">
<td align="center" height="20" width="6%">Full 3D Map</td>
<td align="center" height="20" valign="middle" width="4%"></td>
<td align="center" height="20" valign="middle" width="4%">--</td>
<td align="center" height="20" valign="middle" width="3%">63.41</td>
<td align="center" height="20" valign="middle" width="4%">0.0233</td>
</tr>
<tr>
<td align="center" class="table_head" rowspan="2" width="10%">K. Ninja Original Pid</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="6%">Internal Node Interpolation</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">84.21</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">108.51</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="3%">114.85</td>
<td align="center" class="MI-MDS" height="20" valign="middle" width="4%">0.0247</td>
<td align="center" rowspan="2" valign="middle" width="5%">0.614</td>
<td align="center" rowspan="2" valign="middle" width="5%">0.605</td>
<td align="center" rowspan="2" valign="middle" width="6%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEie0UsMoDHGtWQqQALSkpx6LqC6yuyLIepNlyMyrkYkgaALC965gqBAYzzQOT9kpzUVDGkY3nS1P8vy5lWhj3SraH4-W9qio5h7l9Pg2Tn39AvkRjK2JxoTcrQBKrcGEHBWTUqoTiOSF9-4/s1600/whole-plot-Ninja-Edgesum-Vs-SWG-PIDDensitySat%255B0.85%255D-large_thumb%255B2%255D.png" imageanchor="1"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEie0UsMoDHGtWQqQALSkpx6LqC6yuyLIepNlyMyrkYkgaALC965gqBAYzzQOT9kpzUVDGkY3nS1P8vy5lWhj3SraH4-W9qio5h7l9Pg2Tn39AvkRjK2JxoTcrQBKrcGEHBWTUqoTiOSF9-4/s1600/whole-plot-Ninja-Edgesum-Vs-SWG-PIDDensitySat%255B0.85%255D-large_thumb%255B2%255D.png" height="50" width="50" /></a></td>
<td align="center" rowspan="2" valign="middle" width="6%"></td>
<td align="center" rowspan="2" valign="middle" width="6%">n/a</td>
<td align="center" rowspan="2" valign="middle" width="6%">n/a</td>
<td align="center" class="Plots" rowspan="2" valign="middle" width="7%"><a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/ninja/tree_plot/spherical_phylogram/2133_ninja_pid_origin_distance_sp.pviz">Spherical</a><br />
<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/ninja/tree_plot/rectangular_cladogram/2133_GbWitKruReducedCenters_sideTree_reroot_newColor.pviz">Cuboid</a></td>
<td align="center" rowspan="2" valign="middle" width="6%"><a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/ninja/tree_pdf/swgms_unique_2133_GbWitKruReducedCenters_126RevComp_c%23_reroot.pdf">Rectangle</a></td>
<td align="center" rowspan="2" valign="middle" width="7%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhlcXN9Fw1COPsxNCHA0-fHMJH8_8_p6mkJgBV485J7Q2IprYJ0S2ysvlW1E6T9a-vZA-8hGeD4_MAw8pdYLqNGF_WhcWGFDCJ834Ye_r0pNCRZCT6RtVDkYhILrsvsYm_rLjGWfTpd7OJy/s1600/2133_GbWitKruReducedCenters_sideTree_reroot_newColor.png" imageanchor="1"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhlcXN9Fw1COPsxNCHA0-fHMJH8_8_p6mkJgBV485J7Q2IprYJ0S2ysvlW1E6T9a-vZA-8hGeD4_MAw8pdYLqNGF_WhcWGFDCJ834Ye_r0pNCRZCT6RtVDkYhILrsvsYm_rLjGWfTpd7OJy/s1600/2133_GbWitKruReducedCenters_sideTree_reroot_newColor.png" height="50" width="50" /></a></td>
<td align="center" rowspan="2" valign="middle" width="7%"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhL6pD5LPp__gyQppq9WaaSYkagmRcrWbWOgc58FcItmO_uU3iOGiS8PHnb6Ngu7up7h9tLJBW9rF7R1EpZ-RkmJpMCL6cuWqXEZfb5TcRkdUuU2lSDChjEUpDErPL3MmGRqqH9cKULKo-y/s1600/2133_ninja_pid_origin_distance_sp.png" imageanchor="1"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhL6pD5LPp__gyQppq9WaaSYkagmRcrWbWOgc58FcItmO_uU3iOGiS8PHnb6Ngu7up7h9tLJBW9rF7R1EpZ-RkmJpMCL6cuWqXEZfb5TcRkdUuU2lSDChjEUpDErPL3MmGRqqH9cKULKo-y/s1600/2133_ninja_pid_origin_distance_sp.png" height="50" width="50" /></a></td>
</tr>
<tr class="Manxcat">
<td align="center" height="20" width="6%">Full 3D Map</td>
<td align="center" height="20" valign="middle" width="4%"></td>
<td align="center" height="20" valign="middle" width="4%">--</td>
<td align="center" height="20" valign="middle" width="3%">106.83</td>
<td align="center" height="20" valign="middle" width="4%">0.0224</td>
</tr>
</tbody></table>
<br />
<div style="text-align: center;">
<table border="1" style="text-align: center; width: 300px;">
<caption>
Distance Correlation with Original PID
</caption>
<tbody>
<tr class="table_head">
<th class="table_head" scope="col"></th>
<th scope="col">3D mapping</th>
<th scope="col">10D mapping</th>
</tr>
<tr>
<th class="table_head" scope="row">200 Sequences</th>
<td class="Plots">0.907</td>
<td class="Plots">0.982</td>
</tr>
<tr>
<th class="table_head" scope="row">2133 Sequences</th>
<td class="Plots">0.804</td>
<td class="Plots">0.885</td>
</tr>
</tbody></table>
<br />
<h3 style="text-align: left;">
Robinson-Foulds Metric</h3>
</div>
</ol>
<ul>
<li>Fungi 2133</li>
<ul>
<li>Note. We have made the Ninja 10D transform tree (J) based on data from two MDS programs to verify they agree with each other. The one mentioned in the above table uses the 10 dimensional coordinates generated for each leaf node of the tree using a deterministic annealed (DA) SMACOF MDS program. We have also produced 10 dimensional coordinates for the leaf nodes using a Chisquared MDS program. The tree J is created using Ninja by giving the 10 dimensional Euclidean pairwise distances of leaf nodes. The tree based on former MDS is named as J SMACOF MDS and the other as J Chisq MDS in the below Robinson-Foulds metric.</li>
</ul>
</ul>
<br />
<div>
Reference:</div>
<div>
<li style="font-family: TrebuchetMS, Arial, sans-serif; font-size: 13px; line-height: 16.79599952697754px; list-style: circle; margin-left: 30px; margin-top: 10px;">Yang Ruan, Geoffrey House, Saliya Ekanayake, Ursel Schütte, James D. Bever, Haixu Tang, Geoffrey Fox. <a href="http://salsahpc.indiana.edu/millionseq/reference/Integration%20of%20Clustering%20and%20Multidimensional%20Scaling%20to%20Determine%20Phylogenetic%20Trees%20as%20Spherical%20Phylograms%20Visualized%20in%203%20Dimensions.pdf" style="background-attachment: inherit; background-clip: inherit; background-image: inherit; background-origin: inherit; background-position: inherit; background-repeat: inherit; background-size: inherit; color: #0066b3; text-decoration: none;">Integration of Clustering and Multidimensional Scaling to Determine Phylogenetic Trees as Spherical Phylograms Visualized in 3 Dimensions.</a> Proceedings of C4Bio 2014 of IEEE/ACM CCGrid 2014, Chicago, USA, May 26-29, 2014.</li>
<li style="font-family: TrebuchetMS, Arial, sans-serif; font-size: 13px; line-height: 16.79599952697754px; list-style: circle; margin-left: 30px; margin-top: 10px;">Yang Ruan, Geoffrey Fox. <a href="http://salsahpc.indiana.edu/millionseq/reference/WDA-SMACOF_v1.02.pdf" style="background-attachment: inherit; background-clip: inherit; background-image: inherit; background-origin: inherit; background-position: inherit; background-repeat: inherit; background-size: inherit; color: #0066b3; text-decoration: none;">A Robust and Scalable Solution for Interpolative Multidimensional Scaling with Weighting.</a> Proceedings of IEEE eScience 2013, Beijing, China, Oct. 22-Oct. 25, 2013. (Best Student Innovation Award)</li>
<li style="font-family: TrebuchetMS, Arial, sans-serif; font-size: 13px; line-height: 16.79599952697754px; list-style: circle; margin-left: 30px; margin-top: 10px;">Yang Ruan, Saliya Ekanayake, Mina Rho, Haixu Tang, Seung-Hee Bae, Judy Qiu, Geoffrey Fox. <a href="http://salsahpc.indiana.edu/millionseq/reference/DACIDR_camera_ready_v0.3.pdf" style="background-attachment: inherit; background-clip: inherit; background-image: inherit; background-origin: inherit; background-position: inherit; background-repeat: inherit; background-size: inherit; color: #0066b3; text-decoration: none;">DACIDR: Deterministic Annealed Clustering with Interpolative Dimension Reduction using a Large Collection of 16S rRNA Sequences.</a> Proceedings of ACM-BCB 2012, Orlando, Florida, ACM, Oct. 7-Oct. 10, 2012.</li>
<li style="font-family: TrebuchetMS, Arial, sans-serif; font-size: 13px; line-height: 16.79599952697754px; list-style: circle; margin-left: 30px; margin-top: 10px;">Yang Ruan, Zhenhua Guo, Yuduo Zhou, Judy Qiu, Geoffrey Fox. <a href="http://salsahpc.indiana.edu/millionseq/reference/HyMR_submission_HPDC_workshop_final.pdf" style="background-attachment: inherit; background-clip: inherit; background-image: inherit; background-origin: inherit; background-position: inherit; background-repeat: inherit; background-size: inherit; color: #0066b3; text-decoration: none;">HyMR: a Hybrid MapReduce Workflow System.</a> Proceedings of ECMLS’12 of ACM HPDC 2012, Delft, Netherlands, ACM, Jun. 18-Jun. 22, 2012</li>
<li style="font-family: TrebuchetMS, Arial, sans-serif; font-size: 13px; line-height: 16.79599952697754px; list-style: circle; margin-left: 30px; margin-top: 10px;">Adam Hughes, Yang Ruan, Saliya Ekanayake, Seung-Hee Bae, Qunfeng Dong, Mina Rho, Judy Qiu, Geoffrey Fox. <a href="http://www.biomedcentral.com/1471-2105/13/S2/S9" style="background-attachment: inherit; background-clip: inherit; background-image: inherit; background-origin: inherit; background-position: inherit; background-repeat: inherit; background-size: inherit; color: #0066b3; text-decoration: none;">Interpolative Multidimensional Scaling Techniques for the Identification of Clusters in Very Large Sequence Sets</a>, BMC Bioinformatics 2012, 13(Suppl 2):S9.</li>
</div>
Anonymoushttp://www.blogger.com/profile/12376883776057140162noreply@blogger.com0tag:blogger.com,1999:blog-400445772342786430.post-63853698528006934022012-11-25T12:41:00.002-08:002013-01-12T11:24:42.886-08:00Tree Quality Comparison with Different Measures<br />
<h3>
Abstract</h3>
<div>
In the <a href="http://salsafungiphy.blogspot.com/2012/11/phylogenetic-tree-generation-for.html">Tree Wrap Up Session post</a>, we listed different phylogenetic tree plot created by various multiple sequence alignment method and tree generation method. We have two different dataset, one is 200 sequence set and the other one is 2133 sequence set, used for spherical phylogram and cuboid cladogram. In this post, we use canonical correlation analysis (CCA) and edge sum to compare the quality of these different plot, hopefully could tell the advantages of different methods applied on 3D phylogenetic tree visualization plot.</div>
<h3>
Description</h3>
Environment: Single machine for 200, PolarGrid for 2133 sequences<br />
Aligner: SmithWaterman<br />
ScoringMatrix: EDNAFULL<br />
GapOpen: -16<br />
GapExt: -4<br />
DistanceType: Percentage Identity<br />
Method: all varied<br />
WithReverse: dynamic determine algorithm<br />
Multiple Sequence Alignment: Clustal Omega, Clustal W2 and Muscle<br />
Tree Generation Method: Raxml, Fast Tree, Ninja and Neighbor Joining.<br />
<h3>
Dataset</h3>
<b>1. 200 sequences:</b><br />
1) 126 new centers from fungi454 (id: 0 ~ 125)<br />
2) 74 sequences from GenBank; (id: 126 ~ 199)<br />
<b>2. 2133 sequences:</b><br />
1) 126 new centers from fungi454 (id: 0 ~ 125)<br />
2) 74 sequences from GenBank; (id: 126 ~ 199)<br />
3) 988 unique sequences from Wittiya; (id: 200 ~ 1187, original 1013 sequences)<br />
4) 945 unique sequences from Kruger; (id: 1188 ~ 2132, original 1130 sequences)<br />
<h3>
<b>Tree Configuration</b></h3>
<div style="border: 1px solid rgb(153, 153, 153); height: 200px; overflow: auto; width: 600px;">
<pre>Level configuration: </pre>
<pre>larger size means higher level in tree</pre>
<pre>Color scheme:</pre>
<pre>1) Spherical Phylogram</pre>
<pre>fungi454: <span style="color: lime;">Green</span></pre>
<pre>GenBank: <span style="color: orange;">Orange</span></pre>
<pre>Wittiya<span style="color: orange;">: </span><span style="color: yellow;">Yellow</span></pre>
<pre>Kruger<span style="color: orange;">: </span><span style="color: blue;">Blue</span></pre>
<pre>2) Cuboid Cladogram</pre>
<pre>Colored by branches, 200 sequence set use 20 points per branch, 2133 sequence set use 300 points per branch</pre>
</div>
<br />
<h3>
Tree Evaluation Method</h3>
<div>
We have two ways of comparing the tree quality:<br />
One is to calculate the distance between each pair of leaf nodes using the distance calculation from <a href="https://www.dropbox.com/s/ittd6szln4i7rhs/126%2B74_swg_pid_dasmacof_pidDistance_nj_cp.pviz">here</a>. The distance from leaf node A to leaf node B is the sum of AA and BB. Then we analysis the distance matrix by comparing it to the original distance matrix using CCA. <span style="color: red;">Theoretically if the distance calculation from the tree <b>MAKE SENSE</b>, the correlation should be higher if a tree's quality is better, which we are not sure about the distance calculation method from <a href="http://users.ugent.be/~avierstr/principles/phylogeny.html">here</a>.</span><br />
Another method is to calculate the sum of the edges in the target dimensional space. A cleaner and better looking plot could potentially mean a better phylogenetic tree for analysis. Because the smaller edge sum is, the ancestor of each closed pair of species is closer to them in the target dimension space, which makes sense for evolution theory.<br />
<h3>
Result</h3>
</div>
<div>
From both CCA and Edge Sum comparison the 200 sequences set with all different methods performs well. This means for a small sequence set (hundreds of sequences), either different Multiple Sequence Alignment methods such as Clustal Omega, Clustal W2, Muscle, and tree generation methods such as Neighbor Joining, Ninja, Fast Tree and Raxml doesn't make very much difference. All the methods could successfully determine the phylogeny evolution pattern while not interrupting the original correlations exists in the input species.</div>
<div>
However, when sequence size expands, in our case, to 2133 sequences, the original MSA/Raxml methods performs much worse than Ninja and Neighbor Joining in either CCA and Edge Sum.</div>
<div>
We also notice that Ninja has the same result to Neighbor Joining in the edge sum calculation, which is because these two are basically same methods but Ninja is with a faster approach. And Fast Tree always has a lower edge sum than Raxml, which means it preserves the original correlation better than Raxml for 200 sequence set.</div>
<div>
<h4 style="text-align: center;">
CCA Comparison</h4>
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<h4 style="text-align: center;">
<b> Edge Sum Comparison</b></h4>
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Additional Correlation Comparison between 10D plot distance, 3D plot distance and original pid distance</div>
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Anonymoushttp://www.blogger.com/profile/12376883776057140162noreply@blogger.com0tag:blogger.com,1999:blog-400445772342786430.post-23963978614113115322012-11-20T08:41:00.001-08:002012-11-20T08:41:19.874-08:00Heatmaps of 10D vs 3D vs SWG<p>Here we list heatmaps of distances resulted from dimensional scaling versus original Smith-Waterman for two datasets. The description of distances is as follows.</p> <ul> <li>SWG PID</li> <ul> <li>Percent identity distance calculated from Smith-Waterman local alignment of sequences using EDNAFULL scoring matrix, gap open –16, and gap extension –4. Previous study on SWG PID compared to several other distance measures can be found at <a title="http://salsafungiphy.blogspot.com/2012/10/heatmaps-of-different-distances.html" href="http://salsafungiphy.blogspot.com/2012/10/heatmaps-of-different-distances.html">http://salsafungiphy.blogspot.com/2012/10/heatmaps-of-different-distances.html</a></li></ul> <li>10D</li> <ul> <li>The 10 dimensional Euclidean distance based on DA-SMACOF mapping of SWG PID</li></ul> <li>3D</li> <ul> <li>The 3 dimensional Euclidean distance based on DA-SMACOF mapping of SWG PID</li></ul></ul> <p>The two datasets are described at <a title="http://salsafungiphy.blogspot.com/2012/11/tree-distance-heatmaps.html" href="http://salsafungiphy.blogspot.com/2012/11/tree-distance-heatmaps.html">http://salsafungiphy.blogspot.com/2012/11/tree-distance-heatmaps.html</a></p> <p> </p> <h1>Heatmaps for Fungi 200</h1> <p> </p> <table border="0" cellspacing="0" cellpadding="2" width="400"> <tbody> <tr> <td valign="top" width="200"> <p align="center">3D DA-SMACOF of SWG PID Vs SWG PID</p></td> <td valign="top" width="200"> <p align="center">10D DA-SMACOF of SWG PID Vs SWG PID</p></td></tr> <tr> <td valign="top" width="200"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhlkHf7tCJvyHZxMT8RRbqzEjJ5FDhByFjgSflTztqVan-IgGYLkDhCbtjc7oN1aoRk7PiDp9vsPYkGQiDiEcykUBFTSS0-2yfMCNWaDw13KHC1xGxR4CUGvgmq5_SnyiL2ZACtpLbH7qU/s1600-h/3.%252529whole-plot-DASMACOF-SWG-PID-Vs-SWG-PIDDensitySat%25255B0.85%25255D-large%25255B4%25255D.png"><img style="background-image: none; border-bottom: 0px; border-left: 0px; padding-left: 0px; padding-right: 0px; display: inline; border-top: 0px; border-right: 0px; padding-top: 0px" title="3.)whole-plot-DASMACOF-SWG-PID-Vs-SWG-PIDDensitySat[0.85]-large" border="0" alt="3.)whole-plot-DASMACOF-SWG-PID-Vs-SWG-PIDDensitySat[0.85]-large" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg8sJ28kHghq0dUSc3qajnfsqSGyEXOXD756zzQLlJXKzMP4WxnIwlpXBtyeTVv5NddwnNBtA5TNGp0AfZgvA4x08n4y62evBonwXaJv2hWHitIWBV1Zy7C4QFlLrA8SL4jnC1zcm3UPMA/?imgmax=800" width="480" height="480"></a></td> <td valign="top" width="200"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEggJTxbJ9gYav07_ErQQxu9PdKLE_8SUcHqwCsNNrkfFdwvm-hAEZcXdnIxGQp4ikmgBRqWJ2CIv94l2A8-40XOTn91j6RhTImUnwBCEhn4IZLQTVUtoQdRiBMM8CPZ-bpdbzKBouPwnTw/s1600-h/whole-plot-dasamcof.10D-Vs-swg.pidDensitySat%25255B0.85%25255D-large%25255B6%25255D.png"><img style="background-image: none; border-bottom: 0px; border-left: 0px; padding-left: 0px; padding-right: 0px; display: inline; border-top: 0px; border-right: 0px; padding-top: 0px" title="whole-plot-dasamcof.10D-Vs-swg.pidDensitySat[0.85]-large" border="0" alt="whole-plot-dasamcof.10D-Vs-swg.pidDensitySat[0.85]-large" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj796ECWyPjDWuuWy0CBvnnlMynfl0e7Rxe5IjKP1xXl10iRrXnoSIO0iR3U9wGqWujG9kjoEhWVaYn8FDDhJryUXV7gGTehCpDGnFUZxyzJgmJYEpTCr8_zRl8S6ct0KtiDOI26q_Ffxo/?imgmax=800" width="480" height="480"></a></td></tr> <tr> <td valign="top" width="200"> </td> <td valign="top" width="200"> </td></tr> <tr> <td valign="top" width="200"> </td> <td valign="top" width="200"> </td></tr> <tr> <td valign="top" width="200"> <p align="center">10D DA-SMACOF of SWG PID Vs 3D DA-SMACOF of SWG PID </p></td> <td valign="top" width="200"> </td></tr> <tr> <td valign="top" width="200"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhLQVJCbadTN-OEuM4N47S1R5R2-f1dIS4LaTj1Z3WO6bxHTt_kIPGAPLX_v_KYoZdOgSxpOO0e9YbGXMLm71OgiYfjck85MTgyWDnf1mHGKgD0nRYgQx4ztd6iZfC6rxE9vH-dQCURFK8/s1600-h/whole-plot-dasamcof.10D-Vs-dasmacof.3DDensitySat%25255B0.85%25255D-large%25255B4%25255D.png"><img style="background-image: none; border-bottom: 0px; border-left: 0px; padding-left: 0px; padding-right: 0px; display: inline; border-top: 0px; border-right: 0px; padding-top: 0px" title="whole-plot-dasamcof.10D-Vs-dasmacof.3DDensitySat[0.85]-large" border="0" alt="whole-plot-dasamcof.10D-Vs-dasmacof.3DDensitySat[0.85]-large" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiGOvhyphenhyphenWQ9eEsPvXU08ZDGNob7UFpBsn6CyVh4eh6GJAoqqkSx1DUS747JlrINn60bmCUtqYDipPS38V2sLj9_wDYjjypobjc55A67hURENvtIBN5cEE_QFUnQDWQFJFzEbn8P-DNZfNPM/?imgmax=800" width="480" height="480"></a></td> <td valign="top" width="200"> </td></tr> <tr> <td valign="top" width="200"> </td> <td valign="top" width="200"> </td></tr> <tr> <td valign="top" width="200"> </td> <td valign="top" width="200"> </td></tr></tbody></table> <h1>Heatmaps for Fungi 2133</h1> <table border="0" cellspacing="0" cellpadding="2" width="400"> <tbody> <tr> <td valign="top" width="200"> <p align="center">3D DA-SMACOF of SWG PID Vs SWG PID</p></td> <td valign="top" width="200"> <p align="center">10D DA-SMACOF of SWG PID Vs SWG PID</p></td></tr> <tr> <td valign="top" width="200"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhAY-2cz3vjPcbQ49uq36cMIxhiF8i7cLwxOI41MSaKPK2Eun2tGGRj59ALRZfX__CJDoCmx83uMhcnY3o9tI9DSAoA088_THyu0tB4_rw3rb5BN8u8ikj7PoGAAFWlqeT7aUQwjZVNWdY/s1600-h/whole-plot-DASMACOF-SWG-PID-Vs-SWG-PIDDensitySat%25255B0.85%25255D-large%25255B4%25255D.png"><img style="background-image: none; border-bottom: 0px; border-left: 0px; padding-left: 0px; padding-right: 0px; display: inline; border-top: 0px; border-right: 0px; padding-top: 0px" title="whole-plot-DASMACOF-SWG-PID-Vs-SWG-PIDDensitySat[0.85]-large" border="0" alt="whole-plot-DASMACOF-SWG-PID-Vs-SWG-PIDDensitySat[0.85]-large" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgXoUxyb6wOpcJRJAv01zN6XDHZnt_eWJcV7ua2HR3lWWC1FnRYfl8D6UHCr8chaUD2Xm37wQCx1BEjwzP6BhneUvO5D4VbL9tnqVsT2CMxUoZCh_tzZEJ2XIZhq4DnOTW_Pwp-s-UTNi0/?imgmax=800" width="480" height="480"></a></td> <td valign="top" width="200"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi5L_9jETGsiuBfNsX_-t7xQHSHZxs_tED0bFDGsfCLN2AAxiqlIT6wXh_VMGt69hXvstb5RlpcXoZ1kiI9VL0NbDe0tZjX9ybaGG3UtHYWqf7PRHe3KtzFbyuZxwJcJ68-cRAuL9gD6Ow/s1600-h/whole-plot-dasamcof.10D-Vs-swg.pidDensitySat%25255B0.85%25255D-large%25255B11%25255D.png"><img style="background-image: none; border-bottom: 0px; border-left: 0px; padding-left: 0px; padding-right: 0px; display: inline; border-top: 0px; border-right: 0px; padding-top: 0px" title="whole-plot-dasamcof.10D-Vs-swg.pidDensitySat[0.85]-large" border="0" alt="whole-plot-dasamcof.10D-Vs-swg.pidDensitySat[0.85]-large" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj4x-35RZjt-TFkJejm-1br-Y3_nF0lScWN8bnRtJVZjDEWgxFa8LUi5iMJU1LQp-8gfCUvDbLWvcq66wSfgBzV7hmE7Kz465NV0qTN_aQfrAx8PC4ZclAXiD-pLK-1MwsAt7D_ILEXAPc/?imgmax=800" width="480" height="480"></a></td></tr> <tr> <td valign="top" width="200"> </td> <td valign="top" width="200"> </td></tr> <tr> <td valign="top" width="200"> </td> <td valign="top" width="200"> </td></tr> <tr> <td valign="top" width="200"> <p align="center">10D DA-SMACOF of SWG PID Vs 3D DA-SMACOF of SWG PID </p></td> <td valign="top" width="200"> </td></tr> <tr> <td valign="top" width="200"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj2nMlfojruDyiOzULIcCGknlEv2nYRybjiY_3H2U45Zb3JDDRQ94xF5Tl8K23NPP3Ln71z7K-zKhqb3YkGelrRjbl1IaKZAau3mK4nmvE5hx__do7UnS6hsHNKWUxvt_JyTZw3kN9_MAo/s1600-h/whole-plot-dasamcof.10D-Vs-dasmacof.3DDensitySat%25255B0.85%25255D-large%25255B9%25255D.png"><img style="background-image: none; border-bottom: 0px; border-left: 0px; padding-left: 0px; padding-right: 0px; display: inline; border-top: 0px; border-right: 0px; padding-top: 0px" title="whole-plot-dasamcof.10D-Vs-dasmacof.3DDensitySat[0.85]-large" border="0" alt="whole-plot-dasamcof.10D-Vs-dasmacof.3DDensitySat[0.85]-large" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhZpzFMqbSbYiW-taO7z_UbW8apXvHwsA_xF2EAe-oXO5yulW3wWfRiF_2p2DLBHvbCswjcRJxkJ2LTRQ5et0n4K9dFuO8KKokDsbavTR5rNGMpG0ABodSAWcRJPfh_sxX64xs8utSsxZY/?imgmax=800" width="480" height="480"></a></td> <td valign="top" width="200"> </td></tr> <tr> <td valign="top" width="200"> </td> <td valign="top" width="200"> </td></tr> <tr> <td valign="top" width="200"> </td> <td valign="top" width="200"> </td></tr></tbody></table> Saliya Ekanayakehttp://www.blogger.com/profile/10281589417412608237noreply@blogger.com0tag:blogger.com,1999:blog-400445772342786430.post-8081968166699101822012-11-09T09:03:00.002-08:002012-11-20T11:57:57.337-08:00Phylogenetic Tree Generation for 200/2133 sequences<br />
<h3>
Abstract</h3>
<div>
Traditional phylogenetic tree viewing method includes different graph of following:</div>
<div>
Rectangular phylogram, rectangular cladogram, circular phylogram, circular cladogram, slanted phylogram and slated cladogram.</div>
<div>
All these methods can present the distance from actual sequence (leaf node) to their parents (internal node) precisely. However, there is no way to observe the corrleations between the leaf nodes.</div>
<div>
We proposed a new way of presenting phylogenetic trees, where not only the evolution of the species is shown, but also the relations between different taxas can be observed directly to each other (not through their ancestors). The spherical phylogram and cuboid cladogram (previously called side tree) has been added to our dimension reduction result for thousands of sequences. Not only we used a neighbor joining algorithm to show the structure of the tree based on that, but also we use interpolation for other phylogenetic tree generation method, such as Raxml, Ninja and Fast Tree. </div>
<h3>
Description</h3>
Environment: Single machine for 200, PolarGrid for 2133 sequences<br />
Aligner: SmithWaterman<br />
ScoringMatrix: EDNAFULL<br />
GapOpen: -16<br />
GapExt: -4<br />
DistanceType: Percentage Identity<br />
Method: all varied<br />
WithReverse: dynamic determine algorithm<br />
Multiple Sequence Alignment: Clustal Omega, Clustal W2 and Muscle<br />
Tree Generation Method: Raxml, Fast Tree, Ninja and Neighbor Joining.<br />
<h3>
Dataset</h3>
<b>1. 200 sequences:</b><br />
1) 126 new centers from fungi454 (id: 0 ~ 125)<br />
2) 74 sequences from GenBank; (id: 126 ~ 199)<br />
<b>2. 2133 sequences:</b><br />
1) 126 new centers from fungi454 (id: 0 ~ 125)<br />
2) 74 sequences from GenBank; (id: 126 ~ 199)<br />
3) 988 unique sequences from Wittiya; (id: 200 ~ 1187, original 1013 sequences)<br />
4) 945 unique sequences from Kruger; (id: 1188 ~ 2132, original 1130 sequences)<br />
<h3>
<b>Tree Configuration</b></h3>
<div style="border: 1px solid rgb(153, 153, 153); height: 200px; overflow: auto; width: 600px;">
<pre>Level configuration: </pre>
<pre>larger size means higher level in tree</pre>
<pre>Color scheme:</pre>
<pre>1) Spherical Phylogram</pre>
<pre>fungi454: <span style="color: lime;">Green</span></pre>
<pre>GenBank: <span style="color: orange;">Orange</span></pre>
<pre>Wittiya<span style="color: orange;">: </span><span style="color: yellow;">Yellow</span></pre>
<pre>Kruger<span style="color: orange;">: </span><span style="color: blue;">Blue</span></pre>
<pre>2) Cuboid Cladogram</pre>
<pre>Colored by branches, 200 sequence set use 20 points per branch, 2133 sequence set use 300 points per branch</pre>
</div>
<br />
<h3>
Final Result</h3>
<div>
<b>Speherical Phylogram and Cuboid Cladogram are in pviz format</b>,<i> need to use <a href="http://salsahpc.indiana.edu/pviz3">PlotViz3</a> to open</i>. The <b>Rectangle Cladogram is in pdf format.</b></div>
<b>1. 200 sequence set result:</b><br />
1) Clustal Omega with Fast Tree: <a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/qiime/tree_plot/spherical_phylogram/126+74_clustalOmega_fastTree_sp.pviz">Spherical Phylogram</a>/<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/qiime/tree_plot/cuboid_cladogram/126+74_clustalOmega_fastTree_sideTree.pviz">Cuboid Cladogram</a>/<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/qiime/tree_pdf/126+74_clustalOmega_fastTree.pdf">Rectangle Cladogram</a><br />
2) Clustal Omega with Raxml: <a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/qiime/tree_plot/spherical_phylogram/126+74_clustalOmega_raxml_sp.pviz">Spherical Phylogram</a>/<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/qiime/tree_plot/cuboid_cladogram/126+74_clustalOmega_raxml_sideTree.pviz">Cuboid Cladogram</a>/<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/qiime/tree_pdf/126+74_clustalOmega_raxml.pdf">Rectangle Cladogram</a><br />
3) Clustal W2 with Fast Tree: <a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/qiime/tree_plot/spherical_phylogram/126+74_clustalW2_fastTree_sp.pviz">Spherical Phylogram</a>/<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/qiime/tree_plot/cuboid_cladogram/126+74_clustalW2_fastTree_sideTree.pviz">Cuboid Cladogram</a>/<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/qiime/tree_pdf/126+74_clustalW2_fastTree.pdf">Rectangle Cladogram</a><br />
4) Clustal W2 with Raxml: <a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/qiime/tree_plot/spherical_phylogram/126+74_clustalW2_raxml_sp.pviz">Spherical Phylogram</a>/<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/qiime/tree_plot/cuboid_cladogram/126+74_clustalW2_raxml_sideTree.pviz">Cuboid Cladogram</a>/<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/qiime/tree_pdf/126+74_clustalW2_raxml.pdf">Rectangle Cladogram</a><br />
5) Muscle with Fast Tree: <a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/qiime/tree_plot/spherical_phylogram/126+74_muscle_fastTree_sp.pviz">Spherical Phylogram</a>/<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/qiime/tree_plot/cuboid_cladogram/126+74_muscle_fastTree_sideTree.pviz">Cuboid Cladogram</a>/<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/qiime/tree_pdf/126+74_muscle_fastTree.pdf">Rectangle Cladogram</a><br />
6) Muscle with Raxml: <a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/qiime/tree_plot/spherical_phylogram/126+74_muscle_raxml_sp.pviz">Spherical Phylogram</a>/<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/qiime/tree_plot/cuboid_cladogram/126+74_muscle_raxml_sideTree.pviz">Cuboid Cladogram</a>/<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/qiime/tree_pdf/126+74_muscle_raxml.pdf">Rectangle Cladogram</a><br />
7) Ninja with Original SWG Pid Distance: <a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/ninja/tree_plot/spherical_phylogram/126+74_swg_origin_pid_ninja_sp.pviz">Spherical Phylogram</a>/<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/ninja/tree_plot/cuboid_cladogram/126+74_swg_pid_dasmacof_sideTree_reroot_newcolor.pviz">Cuboid Cladogram</a>/<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/ninja/tree_pdf/126+74__swg_edna_pid_reroot.pdf">Rectangle Cladogram</a><br />
8) Ninja with 10D Pid Distance: <a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/ninja/tree_plot/spherical_phylogram/126+74_swg_10D_plot_distance_ninja_sp.pviz">Spherical Phylogram</a>/<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/ninja/tree_plot/cuboid_cladogram/126+74_10d_dasmacof_reroot_sideTree.pviz">Cuboid Cladogram</a>/<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/ninja/tree_pdf/126+74_swg_origin_10d_reroot.pdf">Rectangle Cladogram</a><br />
9) Neighbor Joining with 3D plot Distance: <a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74/nj/tree_plot/circular_phylogram/126+74_swg_pid_dasmacof_3DplotDistance_nj_cp.pviz">Spherical Phylogram</a><br />
<br />
2. 2133 sequence set result:<br />
1) Clustal Omega 1 iteration with Raxml: <a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/qiime/tree_plot/spherical_phylogram/2133_clustalO_aligned_raxml_sp.pviz">Spherical Phylogram</a>/<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/qiime/tree_plot/rectangular_cladogram/2133_clustalO_aligned_raxml_sideTree.pviz">Cuboid Cladogram</a>/Rectangle Cladogram<br />
2) Clustal Omega 1 iteration (Anna's edition) with Raxml: <a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/qiime/tree_plot/spherical_phylogram/2133_clustalO_anna_aligned_raxml_sp.pviz">Spherical Phylogram</a>/<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/qiime/tree_plot/rectangular_cladogram/2133_clustalO_anna_aligned_raxml_sideTree.pviz">Cuboid Cladogram</a>/Rectangle Cladogram<br />
3) Clustal Omega 10 iterations with Raxml: <a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/qiime/tree_plot/spherical_phylogram/2133_clustalO_aligned_10iter_raxml_sp.pviz">Spherical Phylogram</a>/<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/qiime/tree_plot/rectangular_cladogram/2131_clustalO_aligned_iter10_raxml_sideTree.pviz">Cuboid Cladogram</a>/<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/qiime/tree_pdf/2131_clustalO_10_iter_raxml_reroot_colored.pdf">Rectangle Cladogram</a><br />
4) Clustal Omega 20 iterations with Raxml: <a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/qiime/tree_plot/spherical_phylogram/2133_clustalO_aligned_20iter_raxml_sp.pviz">Spherical Phylogram</a>/<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/qiime/tree_plot/rectangular_cladogram/2133_clustalO_aligned_20iter_raxml_sideTree.pviz">Cuboid Cladogram</a>/<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/qiime/tree_pdf/2131_clustalO_20_iter_raxml_reroot_colored.pdf">Rectangle Cladogram</a><br />
5) Muscle 2 iterations with Raxml: <a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/qiime/tree_plot/spherical_phylogram/2133_muscle_aligned_raxml_sp.pviz">Spherical Phylogram</a>/<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/qiime/tree_plot/rectangular_cladogram/2133_muscle_aligned_sideTree_reroot_newColor.pviz">Cuboid Cladogram</a>/<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/qiime/tree_pdf/2133_muscle_aligned_reroot.pdf">Rectangle Cladogram</a><br />
6) Ninja with Original SWG Pid Distance: <a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/ninja/tree_plot/spherical_phylogram/2133_ninja_pid_origin_distance_sp.pviz">Spherical Phylogram</a>/<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/ninja/tree_plot/rectangular_cladogram/2133_GbWitKruReducedCenters_sideTree_reroot_newColor.pviz">Cuboid Cladogram</a>/<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/ninja/tree_pdf/swgms_unique_2133_GbWitKruReducedCenters_126RevComp_c%23_reroot.pdf">Rectangle Cladogram</a><br />
7) Ninja with 3D plot Distance: <a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/ninja/tree_plot/spherical_phylogram/2133_ninja_pid_3D_plot_distance_sp.pviz">Spherical Phylogram</a>/<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/ninja/tree_plot/rectangular_cladogram/2133_swg_pid_dasmacof_grouped_3d_dist_sideTree.pviz">Cuboid Cladogram</a>/<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/ninja/tree_pdf/2133_swg_pid_dasmacof_grouped_3d_dist_reroot_colored.pdf">Rectangle Cladogram</a><br />
8) Ninja with 10d Pid Distance: <a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/ninja/tree_plot/spherical_phylogram/2133_ninja_pid_10d_distance_sp.pviz">Spherical Phylogram</a>/<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/ninja/tree_plot/rectangular_cladogram/2133_10d_dist_reroot_ninja_sideTree.pviz">Cuboid Cladogram</a>/<a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/ninja/tree_pdf/dasmacof.2133.10d.ninja.reroot.pdf">Rectangle Cladogram</a><br />
9) Neighbor Joining with 3D plot Distance: <a href="http://salsahpc.indiana.edu/PhylogeneticTree/phylo_tree/126+74+1016+1130/nj/tree_plot/spherical_phylogram/2133_swg_pid_nj_sp.pviz">Spherical Phylogram</a><br />
<h3>
Screen Shot</h3>
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With PlotViz, we are able to show sequences in a spherical phylogram with their name shown or not, here is a screen shot from 200 sample neighbor joining algorithm from 3D plot distance:</div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgyUvkxUOYslXbCPu4yI2FeygHzyteQwodhxSvIwrgOT51Ag0KkRLqaDM0Wr4z5WoK5a8Vs8tTrnCfP7YqmGH-2XC2JJOWhZjJcR3lYKFfeUWR2zcjEbhIXYc5Ic0VDicDWaum3AB-gHHuf/s1600/126+74_swg_pid_dasmacof_3DplotDistance_nj_cp.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgyUvkxUOYslXbCPu4yI2FeygHzyteQwodhxSvIwrgOT51Ag0KkRLqaDM0Wr4z5WoK5a8Vs8tTrnCfP7YqmGH-2XC2JJOWhZjJcR3lYKFfeUWR2zcjEbhIXYc5Ic0VDicDWaum3AB-gHHuf/s1600/126+74_swg_pid_dasmacof_3DplotDistance_nj_cp.png" height="270" width="400" /></a></div>
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The cuboid plot from Ninja using 3D plot distance is shown as below:<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgLgkUo8JqZ6SzIDJixScE4rOIgF6vQVGjWaQ0wpeJKBkI6YpNPRV0vsITft0Le9Rgb_F9rbkWa_MDsVAyNUPZNK5bMnXVnnFsBycISlEY0RWsA_ubeEblhBCdqdIc2AItHmkOjtWT0Z1qq/s1600/2133_swg_pid_dasmacof_grouped_3d_dist_sideTree.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgLgkUo8JqZ6SzIDJixScE4rOIgF6vQVGjWaQ0wpeJKBkI6YpNPRV0vsITft0Le9Rgb_F9rbkWa_MDsVAyNUPZNK5bMnXVnnFsBycISlEY0RWsA_ubeEblhBCdqdIc2AItHmkOjtWT0Z1qq/s1600/2133_swg_pid_dasmacof_grouped_3d_dist_sideTree.png" height="220" width="400" /></a></div>
Part of the cuboid tree can be hidden to make some more interesting branches shown in a clear fashion:<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgWe3z92Tk-fYs6i0grS0tH6sB-2WdqjLbmoSPSVASNVqbCpu4uZAm3JlDYEV30FrF5nPJY3UHHt8m5E4HWmhGp3S7nu8DaOJUS7-9gkCOEB8h8I3-t6H_DYu7mjeEcXvAjkeaKi0-l_FWy/s1600/2133_swg_pid_dasmacof_grouped_3d_dist_sideTree_part.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgWe3z92Tk-fYs6i0grS0tH6sB-2WdqjLbmoSPSVASNVqbCpu4uZAm3JlDYEV30FrF5nPJY3UHHt8m5E4HWmhGp3S7nu8DaOJUS7-9gkCOEB8h8I3-t6H_DYu7mjeEcXvAjkeaKi0-l_FWy/s1600/2133_swg_pid_dasmacof_grouped_3d_dist_sideTree_part.png" height="248" width="400" /></a></div>
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Anonymoushttp://www.blogger.com/profile/12376883776057140162noreply@blogger.com4tag:blogger.com,1999:blog-400445772342786430.post-81756064398395331392012-11-05T12:40:00.001-08:002012-11-14T22:02:38.273-08:00Tree Distance HeatmapsThis is an attempt to find a “goodness” measure for phylogenetic trees generated by programs such as Ninja (<a href="http://nimbletwist.com/software/ninja/index.html">http://nimbletwist.com/software/ninja/index.html</a>) or RAxML (<a href="http://www.phylo.org/news/RAxML">http://www.phylo.org/news/RAxML</a>). We calculate distance, which we refer as “Tree Distance”, for each pair of sequences based on the structure of the tree. We then compare this against original pairwise distances computed for sequences based on either local alignment or multiple sequence alignment. Definition for tree distance is not unique and we currently use the “Edge Sum” definition given below. Edge Count is possibly another definition to test, though we have not tested it yet.<br> <ul> <li>Edge Sum <ul> <li>Given two sequence A and B, we find the shortest path from A to B in the tree and sum up values on edges along the path. </li></ul> <li>Edge Count <ul> <li>Given two sequence A and B, we find the shortest path from A to B and count the number of edges in it.</li></ul></li></ul>We have performed this analysis for two datasets.<br> <ul> <li>Fungi 200 <a title="https://www.sugarsync.com/pf/D6858752_2739277_6854163" href="https://www.sugarsync.com/pf/D6858752_2739277_6854163">https://www.sugarsync.com/pf/D6858752_2739277_6854163</a> <ul> <li>126 sequences (in reverse complemented form) represent the centers for clusters in <a href="http://salsahpc.indiana.edu/millionseq/haixu/fungi_index.html">http://salsahpc.indiana.edu/millionseq/haixu/fungi_index.html</a> (note. restricted access) <li>74 sequences from GenBank</li></ul> <li>Fungi 2133 <a title="https://www.sugarsync.com/pf/D6858752_0743775_6281705" href="https://www.sugarsync.com/pf/D6858752_0743775_6281705">https://www.sugarsync.com/pf/D6858752_0743775_6281705</a> <ul> <li>126 sequences (in reverse complemented form) represent the centers for clusters in <a href="http://salsahpc.indiana.edu/millionseq/haixu/fungi_index.html">http://salsahpc.indiana.edu/millionseq/haixu/fungi_index.html</a> (note. restricted access) <li>74 sequences from GenBank <li>988 sequences from Kruger et. al. dataset <li>945 sequences from Wittiya’s dataset</li></ul></li></ul><br> <h1>Heatmaps for Fungi 200 </h1> <table style="width: 400px" border="0" cellspacing="0" cellpadding="2"> <tbody> <tr> <td valign="top" width="243"> <div align="center">3D DA-SMACOF of SWG PID Vs SWG PID</div></td> <td valign="top" width="157"> </td></tr> <tr> <td valign="top" width="243"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiFhl-b32V96wcS8UtILtREu4XzMBfiX4ElFzCTTgTY4vJ5dbmZBllPVZBMPZ5jriZQU4SN_f8LwbPK0613YXme01lnFOYqcRkv1IQeerax6oMzclkhM3E_M8Cyz-u9v9mn-Bj4Flz5yIA/s1600-h/3.%252529whole-plot-DASMACOF-SWG-PID-Vs-SWG-PIDDensitySat%25255B0.85%25255D-large%25255B9%25255D.png"><img style="background-image: none; border-right-width: 0px; padding-left: 0px; padding-right: 0px; display: inline; border-top-width: 0px; border-bottom-width: 0px; border-left-width: 0px; padding-top: 0px" title="3.)whole-plot-DASMACOF-SWG-PID-Vs-SWG-PIDDensitySat[0.85]-large" border="0" alt="3.)whole-plot-DASMACOF-SWG-PID-Vs-SWG-PIDDensitySat[0.85]-large" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhR7la9PFAEhbqSRt3gLWM2ACujY9KMVlzNf-dqJUv7O5hoDJq-SRpBWBynP_GJ3xlkl7bZyCojVAjVTxRpRzKML8HtWZ-7ZmloihW6DBiVAlkivYoOw5mXJcANuvAJjBcUR6iDA5PUNiY/?imgmax=800" width="480" height="480"></a></td> <td valign="top" width="157"> </td></tr> <tr> <td valign="top" width="243"> </td> <td valign="top" width="157"> </td></tr> <tr> <td valign="top" width="243"> </td> <td valign="top" width="157"> </td></tr> <tr> <td valign="top" width="243"> </td> <td valign="top" width="157"> </td></tr> <tr> <td valign="top" width="243"> <div align="center">Edge Sum Ninja from SWG PID Vs 3D DA-SMACOF of SWG PID</div></td> <td valign="top" width="157"> <div align="center">Edge Sum Ninja from SWG PID Vs SWG PID</div></td></tr> <tr> <td valign="top" width="243"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjdNk7umF2NPKOfVhSOmQr27PiZ6YfJH9WnBi4cSPwgCGtRPZEFDtXQjC9R5XrRoFYxLpa4OAxTz-kPTbuD55g1WpTUPNtlvqvhoi8w6p95LGnmqEqdVk7du_xITYYqvIClWhZNZMuMdcA/s1600-h/1.%252529whole-plot-Ninja-Edgesum-Vs-DASMACOF-SWG-PIDDensitySat%25255B0.85%25255D-large%25255B4%25255D.png"><img style="background-image: none; border-right-width: 0px; padding-left: 0px; padding-right: 0px; display: inline; border-top-width: 0px; border-bottom-width: 0px; border-left-width: 0px; padding-top: 0px" title="1.)whole-plot-Ninja-Edgesum-Vs-DASMACOF-SWG-PIDDensitySat[0.85]-large" border="0" alt="1.)whole-plot-Ninja-Edgesum-Vs-DASMACOF-SWG-PIDDensitySat[0.85]-large" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiM7Bjak9dLt_X8Qvl3rvL1rjanlnI9m1xGC79QbyAwgMEKkmFX13usf1vcpaKQcHJBLUgXHgmdcy-C0sRO3igUY5UQ8lakuKyreL1IMwT07SvLXc6phdotaHqdFyJJ_REQpER7OLsB6kc/?imgmax=800" width="480" height="480"></a></td> <td valign="top" width="157"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiNPfroEqWS3H_3b0W29xNmzDnL2wuCGuhWNAqvDysaBtI_5mQA4JaB07syACZmAsJMcwHPoWSaXMnpgqZA93EClFCR5PeEHiHBlVk-nsr3RPQbIlvE1opnnHlaCRUq47pn7QT9yXcNAOI/s1600-h/2.%252529whole-plot-Ninja-Edgesum-Vs-SWG-PIDDensitySat%25255B0.85%25255D-large%25255B4%25255D.png"><img style="background-image: none; border-right-width: 0px; padding-left: 0px; padding-right: 0px; display: inline; border-top-width: 0px; border-bottom-width: 0px; border-left-width: 0px; padding-top: 0px" title="2.)whole-plot-Ninja-Edgesum-Vs-SWG-PIDDensitySat[0.85]-large" border="0" alt="2.)whole-plot-Ninja-Edgesum-Vs-SWG-PIDDensitySat[0.85]-large" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEikRSJbCi6n6lge4M-LEOKCtXb2EOthjQsAA_oNJnLCiU3ZL8vv9B4ZXbbweJoDhwhHRDjfhfqdSDNXNGe-FcEqORbpyhcByYOpKVXYeGIonK1HmJoNNpLdLUgXvUV02n7ACbbjMEOTu6Y/?imgmax=800" width="480" height="480"></a></td></tr></tbody></table><br> <h1>Heatmaps of Fungi 2133</h1> <table style="width: 400px" border="0" cellspacing="0" cellpadding="2"> <tbody> <tr> <td valign="top" width="200"> <div align="center">3D DA-SMACOF of SWG PID Vs SWG PID</div></td> <td valign="top" width="200"> </td></tr> <tr> <td valign="top" width="200"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhYSl-ZhNhyphenhyphencjLkOCwu4-ryEa_neq_Rf9Ez16Ocds4n25g644WzOJsiQGaySXcl2VCPvI9184yGldD4iC_5Nduk69RSHPZGKHO5TPG6yU4FcNGHeX1b3LyLyaNdAldl6Em8hI3zB-KOd4w/s1600-h/whole-plot-DASMACOF-SWG-PID-Vs-SWG-PIDDensitySat%25255B0.85%25255D-large%25255B4%25255D.png"><img style="background-image: none; border-right-width: 0px; padding-left: 0px; padding-right: 0px; display: inline; border-top-width: 0px; border-bottom-width: 0px; border-left-width: 0px; padding-top: 0px" title="whole-plot-DASMACOF-SWG-PID-Vs-SWG-PIDDensitySat[0.85]-large" border="0" alt="whole-plot-DASMACOF-SWG-PID-Vs-SWG-PIDDensitySat[0.85]-large" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjmL2datQwNSSVUouf1aGa4e-NdMvbW_RFRgvzsbeFiPMWCYT1TbFFp1o4Z1a3piO4dg0nmyPCS5k1AovitoTYp3tMAQZkv54xpxylmqPImHUbr6a31usTcDfuakCVk-0NvjNMxbG9Imbk/?imgmax=800" width="480" height="480"></a></td> <td valign="top" width="200"> </td></tr> <tr> <td valign="top" width="200"> </td> <td valign="top" width="200"> </td></tr> <tr> <td valign="top" width="200"> </td> <td valign="top" width="200"> </td></tr> <tr> <td valign="top" width="200"> </td> <td valign="top" width="200"> </td></tr> <tr> <td valign="top" width="200"> <div align="center">Edge Sum Ninja from 3D DA-SMACOF of SWG PID Vs 3D DA-SMACOF of SWG PID</div></td> <td valign="top" width="200"> <div align="center">Edge Sum Ninja from 3D DA-SMACOF of SWG PID Vs SWG PID</div></td></tr> <tr> <td valign="top" width="200"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhNh6GZqhXs7huvAOS3wW5-2iG-0zz3pG9iwHMHqCkKoXb0m_CAmiRR32zp8JsG6uxa8EBZow8V4byX0VdYR1Y_5hazj6GgEpvMLxlZ6A8vfnryKRDg1jOb6zzZpva_JkXbKv33qHfhL0I/s1600-h/whole-plot-Ninja-Edgesum-Vs-DASMACOF-SWG-PIDDensitySat%25255B0.85%25255D-large%25255B4%25255D.png"><img style="background-image: none; border-right-width: 0px; padding-left: 0px; padding-right: 0px; display: inline; border-top-width: 0px; border-bottom-width: 0px; border-left-width: 0px; padding-top: 0px" title="whole-plot-Ninja-Edgesum-Vs-DASMACOF-SWG-PIDDensitySat[0.85]-large" border="0" alt="whole-plot-Ninja-Edgesum-Vs-DASMACOF-SWG-PIDDensitySat[0.85]-large" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgCuG5lwo3nmq-RLNE2Oai1qesvOFR1MSu5BYYKksI_AhDEjP_b6935E1EDzrFzAxiOEyst-_vInE1ZfwESoqRA33SQ3xBqE-0iBaEqiAHwrjA-w3ln6IQVr1yDe97dHNS0-ShHxPGAB9k/?imgmax=800" width="480" height="480"></a></td> <td valign="top" width="200"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj22H_vBSNtqYb5R1hrShA-2OywD0kRW296hyphenhyphenFY4pKiajgy4jPypXZXyHcz_ym-DHJXnpdWSCKDkVHPyRUkW0aQIMYeYWzCXf993b4pkh1Ip3U7jXsVrTskfzj7buTRDxNJEVcSHGoEK7s/s1600-h/whole-plot-Ninja-Edgesum-Vs-SWG-PIDDensitySat%25255B0.85%25255D-large%25255B4%25255D.png"><img style="background-image: none; border-right-width: 0px; padding-left: 0px; padding-right: 0px; display: inline; border-top-width: 0px; border-bottom-width: 0px; border-left-width: 0px; padding-top: 0px" title="whole-plot-Ninja-Edgesum-Vs-SWG-PIDDensitySat[0.85]-large" border="0" alt="whole-plot-Ninja-Edgesum-Vs-SWG-PIDDensitySat[0.85]-large" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhO8mL4pAXWpoET8QEP4qwEX7UmjyfyPjCVSF4Y0vEGhsHyH7PngQWAz4Bn5YZrY2WZwEkWsDGAbbKUmecAnxil4oKM0_LjeZl-qNA7ztwAl4-1tbdKpDp1w4iLN3hlO6gS8GWDzOIhvgk/?imgmax=800" width="480" height="480"></a></td></tr> <tr> <td valign="top" width="200"> </td> <td valign="top" width="200"> </td></tr> <tr> <td valign="top" width="200"> </td> <td valign="top" width="200"> </td></tr> <tr> <td valign="top" width="200"> </td> <td valign="top" width="200"> </td></tr> <tr> <td valign="top" width="200"> <div align="center">Edge Sum RAxML(20 iterations) from ClustlO MSA Vs SWG PID</div></td> <td valign="top" width="200"> <div align="center">Edge Sum RAxML (20 iterations) from ClustlO MSA (distances from 0 to 0.15) Vs SWG PID </div></td></tr> <tr> <td valign="top" width="200"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhePQ12flukgz7Q8B73BGCAmWeAAWeDHYCjitm7IsYRzUsgtfk5A9-kSDeKTS8lsTSe9PMc367ELwMxUn1MaW2auCvrMMlbdaadNH-qbcSk7l4k0gGjMC6HC38DruV-K-MyPSYYSC5PvyQ/s1600-h/whole-plot-Raxml%25252820%252529ClustlO-Edgesum-Vs-SWG-PIDDensitySat%25255B0.85%25255D-large-1%25255B4%25255D.png"><img style="background-image: none; border-right-width: 0px; padding-left: 0px; padding-right: 0px; display: inline; border-top-width: 0px; border-bottom-width: 0px; border-left-width: 0px; padding-top: 0px" title="whole-plot-Raxml(20)ClustlO-Edgesum-Vs-SWG-PIDDensitySat[0.85]-large-1" border="0" alt="whole-plot-Raxml(20)ClustlO-Edgesum-Vs-SWG-PIDDensitySat[0.85]-large-1" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEifQ17ecE0sqrrtdwLCbsjD4_onyUE2q3hw9lx7EzvhcTdUnp9pllb4utyIncdqhuTmzVrj_VWgc3WA3Eb5_6drdrUdIjuPjgYODVh5175Oxy51A4m1QD6qlOlOv6n9Nkyn9HQBDBsYz5I/?imgmax=800" width="480" height="480"></a></td> <td valign="top" width="200"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEioQARhITaQJBRnUWpgfyBHw29Hb_5GNRbKvAUAjvmAduSaKqNaN1iahJL9UXBIbZhMhhr9p6vo52k7splpt6jstKpwdxRpiHMl3Tcui4Z7OWqapZhRD38_-E9F6pFfUzLc0pCjI5p8RCA/s1600-h/whole-plot-Raxml%25252820%252529ClustlO-Edgesum-Vs-SWG-PIDDensitySat%25255B0.85%25255D-large-2%25255B4%25255D.png"><img style="background-image: none; border-right-width: 0px; padding-left: 0px; padding-right: 0px; display: inline; border-top-width: 0px; border-bottom-width: 0px; border-left-width: 0px; padding-top: 0px" title="whole-plot-Raxml(20)ClustlO-Edgesum-Vs-SWG-PIDDensitySat[0.85]-large-2" border="0" alt="whole-plot-Raxml(20)ClustlO-Edgesum-Vs-SWG-PIDDensitySat[0.85]-large-2" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgaNUFwbRs63FaAw_oLklmAmwFGy0z8sySiBKMS2qIFA9I8uUcl_GlsOILiyB72BX928D291_ETmjJn3x-jFF-b7Y7tgpjvuts-Sh3_N4c2gp87ZnRUhVcG8yLM160lgEvb0JQVh3l_5wo/?imgmax=800" width="480" height="480"></a></td></tr> <tr> <td valign="top" width="200"> </td> <td valign="top" width="200"> </td></tr> <tr> <td valign="top" width="200"> </td> <td valign="top" width="200"> </td></tr> <tr> <td valign="top" width="200"> </td> <td valign="top" width="200"> </td></tr> <tr> <td valign="top" width="200"> <div align="center">Edge SumRAxML(20 iterations) from ClustlO MSA Vs Strict PIDNG</div></td> <td valign="top" width="200"> <div align="center">Edge Sum RAxML (20 iterations) from ClustlO MSA (distances from 0 to 0.15) Vs Strict PIDNG</div></td></tr> <tr> <td valign="top" width="200"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhjT3lJks0eYJ7LkXxsYQqV71B2hBEOTC4CObsHfJKZNXBDgzSvOS54D_KlKzjXlwk_F5euB5I-dZfZ39fYSAb2wxdYP9bkf3Jde3R_98B5_TPbrs3bhsmCHWCHmAQxlFRzkbtpIbtwndE/s1600-h/whole-plot-Raxml%25252820%252529ClustlO-Edgesum-Vs-Strict-PIDNGDensitySat%25255B0.85%25255D-large-1%25255B4%25255D.png"><img style="background-image: none; border-bottom: 0px; border-left: 0px; padding-left: 0px; padding-right: 0px; display: inline; border-top: 0px; border-right: 0px; padding-top: 0px" title="whole-plot-Raxml(20)ClustlO-Edgesum-Vs-Strict-PIDNGDensitySat[0.85]-large-1" border="0" alt="whole-plot-Raxml(20)ClustlO-Edgesum-Vs-Strict-PIDNGDensitySat[0.85]-large-1" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEizzpYDTbgtTObs7kRV5yvCGvn0m21iSzvC_pCizfgndWvMr1591_JJo901OwOJPbXxf_AA6gnQEhwZDKDTIK4-mSH877SjGRcMQh_OmuLHLDBVO8SumXcBYs-X61K-pLYIcsar8qyOP_4/?imgmax=800" width="480" height="480"></a></td> <td valign="top" width="200"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhhNIQV0W0yOmLTmQOzQRLgvjfYJDVL-rj3Fk8zCt0rsmQYZTWQeJsn1gY5fuZEs9epXpFi_2Vi8dg_CsXJ8cnD04kJhAchJQtZgxpIYWuzon9x11F8zo2TetxYwuiTQZUYKbyWjlwn5oo/s1600-h/whole-plot-Raxml%25252820%252529ClustlO-Edgesum-Vs-Strict-PIDNGDensitySat%25255B0.85%25255D-large-2%25255B4%25255D.png"><img style="background-image: none; border-bottom: 0px; border-left: 0px; padding-left: 0px; padding-right: 0px; display: inline; border-top: 0px; border-right: 0px; padding-top: 0px" title="whole-plot-Raxml(20)ClustlO-Edgesum-Vs-Strict-PIDNGDensitySat[0.85]-large-2" border="0" alt="whole-plot-Raxml(20)ClustlO-Edgesum-Vs-Strict-PIDNGDensitySat[0.85]-large-2" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgEQBRgzSoEZ4piXT_Ju-WQjbsWyj2m1BSyFT6u7voN3CPg-et5kGDzaOkvDURYkS85IJ4ksEsQ36W2TpAl-gDULxvBIMJdGJuHrBfc4JY_IsyDsncyb4zPIVPJFgeGM6vFdG65MdToeCE/?imgmax=800" width="480" height="480"></a></td></tr></tbody></table> Saliya Ekanayakehttp://www.blogger.com/profile/10281589417412608237noreply@blogger.com0tag:blogger.com,1999:blog-400445772342786430.post-59460048693904252602012-10-24T13:44:00.001-07:002012-10-24T14:07:58.509-07:00Pairwise Distances from Multiple Sequence Alignment (MSA) Vs Pairwise Local Alignment DistancesHere we have compared the pairwise distances calculated from a multiple sequence alignment (MSA) file versus pairwise distances calculated from the local pairwise alignment of sequences.<br />
The comparison is based on the sequences found <a href="https://www.sugarsync.com/pf/D6858752_0743775_6121095?directDownload=True">here</a>. MSA corresponding to this can be found <a href="https://www.sugarsync.com/pf/D6858752_0743775_6112447?directDownload=True">here</a>. <br />
<ul>
<li>Distances</li>
<ul>
<li>We computed the percent identity excluding gaps (PIDNG) distance for each pair of aligned sequences in the MSA file. The formula is to count the number of identical base pairs and divide it by the total number base pairs. Each base pair should have characters belonging to the given alphabet to be considered in the computation. To convert this value to represent the distance between two sequences we subtract it from 1.0. </li>
<ul>
<li>PIDNG Distance = 1.0 – PIDNG </li>
<li>where PIDNG = # Identical Pairs / # Pairs and both characters in each pair belongs to the given alphabet.</li>
</ul>
<li>We compute percent identity (PID) distance for each pair of sequences in the original sequence (FastA) file after aligning them locally using Smith-Waterman algorithm. For a given alignment of the two sequences, PID is calculated similarly to PIDNG except those pairs whose one character is a gap are also counted towards the total number of pairs in the alignment. Similar to PIDNG distance we take the 1.0 – PID to get PID distance.</li>
<ul>
<li>PID Distance = 1.0 – PID</li>
<li>where PID = # Identical Pairs / # Pairs</li>
</ul>
</ul>
<li>Alphabet</li>
<ul>
<li>Strict DNA</li>
<ul>
<li>Considers only A, C, T, G characters</li>
</ul>
<li>Full DNA</li>
<ul>
<li>Considers A, C, M, G, R, S, V, T, W, Y, H, K, D, B, N characters</li>
</ul>
<li>We computed PIDNG distance for MSA file using both alphabets</li>
<li>We computed PID distance for locally aligned sequences using Full DNA, but excluding character N.</li>
</ul>
<li>Smith-Waterman Parameters</li>
<ul>
<li>Scoring Matrix</li>
<ul>
<li>EDNAFULL</li>
</ul>
<li>Penalties</li>
<ul>
<li>Gap open = –16 and gap extension = – 4 </li>
</ul>
</ul>
<li>Heatmaps</li>
</ul>
<table border="0" cellpadding="2" cellspacing="0" style="width: 1556px;"> <tbody>
<tr> <td valign="top" width="774"><div align="center">
Strict DNA Alphabet for MSA PIDNG Calculation</div>
</td> <td valign="top" width="26"></td> <td valign="top" width="757"><div align="center">
Full DNA Alphabet for MSA PIDNG Calculation</div>
</td></tr>
<tr> <td valign="top" width="774"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjlK8lsnuv4TEAKMd3b2k7p8KCQMtV_FYGTe4V3OWk8EnjGNlAbGl3cUu5CghkJRlJt8HAjpeweJxJ9tIZNfA0m4RSMXWdk-nXZnAIYhpSu3fVtChJJGN7qdPzQ2RkKjcVJpCaWoDSVG48/s1600-h/whole-plot-MSA-PIDNG-Vs-Pairwise-SWG-PIDDensitySat%25255B0.85%25255D-large%25255B19%25255D.png"><img alt="whole-plot-MSA-PIDNG-Vs-Pairwise-SWG-PIDDensitySat[0.85]-large" border="0" height="768" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjUTPMrW9kv8ClFJ-Bc_BucukbMCPZ60Z0vVjxT3JeOHw3_UDJOLGB2HicNbFuYLtIwqrofiMA3eskxD4XJEY420bI1f96arYuGaVy9JRUmm-b33pg41OEeD6zZUDxuE7v81Ygq-baX_X0/?imgmax=800" style="background-image: none; border-bottom: 0px; border-left: 0px; border-right: 0px; border-top: 0px; display: inline; padding-left: 0px; padding-right: 0px; padding-top: 0px;" title="whole-plot-MSA-PIDNG-Vs-Pairwise-SWG-PIDDensitySat[0.85]-large" width="768" /></a></td> <td valign="top" width="26"></td> <td valign="top" width="757"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjcRK73Gseu4jA_Vzf7JnlddaRTvpXzQntHqI8O8oPUVi5GcSSs5NNtN2mepNEf5vBV674GxwfcoevxUjjAZTMZxurKuYdR6vkgFLLxGJS4UAziy9q5pfdtBsruehLStFRQ-QyRIHeAZQA/s1600-h/whole-plot-MSA-PIDNG-Vs-Pairwise-SWG-PIDDensitySat%25255B0.85%25255D-large%25255B24%25255D.png"><img alt="whole-plot-MSA-PIDNG-Vs-Pairwise-SWG-PIDDensitySat[0.85]-large" border="0" height="768" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg8Z3QclA_uRkqqPuRkf33URTO_rpWd86NLRuVdq57E3rWzoYU5R6Yrv42-qeTrcv-6_X2EfpzVx1OKw-20_IagWXS0mwE4_YttW98-FYCCtEeMp-P5i6euhbPMPGAj_wK7gX8mQddAiTM/?imgmax=800" style="background-image: none; border-bottom: 0px; border-left: 0px; border-right: 0px; border-top: 0px; display: inline; padding-left: 0px; padding-right: 0px; padding-top: 0px;" title="whole-plot-MSA-PIDNG-Vs-Pairwise-SWG-PIDDensitySat[0.85]-large" width="768" /></a></td></tr>
</tbody></table>
Saliya Ekanayakehttp://www.blogger.com/profile/10281589417412608237noreply@blogger.com0tag:blogger.com,1999:blog-400445772342786430.post-28924032261591998842012-10-08T09:04:00.001-07:002012-10-08T14:59:20.100-07:00Heatmaps of Different Distances<ul>
<li><span style="font-size: small;">The type of distances</span> <ul>
<li>PID – #-of-matches / alignment-length-including-gaps-in-the-middle </li>
<li>AvgLocal – Score(A,B) / Avg (Score(A’A’), Score(B’,B’)) where A’ and B’ indicate the aligned regions in the original A and B sequences </li>
<li>MaxGlobal – Score(A,B) / Max(Score(A,A), Score(B,B)) </li>
<li>MaxLocal – Score(A,B) / Max(Score(A’A’, B’B’) </li>
<li>MinGlobal – Score(A,B) / Min(Score(A,A), Score(B,B)) </li>
<li>MinLocal – Score(A,B) / Min(Score(A’A’), Score(B’B’))</li>
</ul>
</li>
</ul>
<br />
<ul>
<li><span style="font-size: small;">Heatmaps for vs PID</span></li>
</ul>
<table border="0" cellpadding="2" cellspacing="0" style="width: 968px;"> <tbody>
<tr> <td valign="top" width="463"><ul> <ul>
<li><strong>AvgLocal Vs PID</strong></li>
</ul>
</ul>
</td> <td valign="top" width="503"><ul> <ul>
<li><strong>MaxGlobal Vs PID </strong></li>
</ul>
</ul>
</td></tr>
<tr> <td valign="top" width="463"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjBfVq40KEWPyAfqtNksSadyE9AylEzuCBg10lHiZbkHiKG9FzF8z-YmiKjanL6FjGWZLrCU1s8pCvF2dIG1J4T5YwwB5jntXEIchR5k4dno8XCUyPMfjV2ILXBHxe90DIr9Zclo2KpVZU/s1600-h/whole-plot-SWG-AvgLocal-Vs-SWG-PIDDe.png"><img alt="whole-plot-SWG-AvgLocal-Vs-SWG-PIDDensitySat[0.85]-large" border="0" height="480" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjZKitKdWqaoYVz9MfjjR0dUMRlxw0zsHCwCwZ3_k7LdJGDeVx9Ia5fjUitEvAutBMeFaGHJdHJRio7G6LgaEIk0rJv5QkfTYwwt1Aa_8gmlfoKIijyhvj9GD9MHcUIDTlaUEB3u8KdgOo/?imgmax=800" style="background-image: none; border-bottom-width: 0px; border-left-width: 0px; border-right-width: 0px; border-top-width: 0px; display: inline; padding-left: 0px; padding-right: 0px; padding-top: 0px;" title="whole-plot-SWG-AvgLocal-Vs-SWG-PIDDensitySat[0.85]-large" width="480" /></a></td> <td valign="top" width="503"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgENhP5MRq8CU6wPYq8JmXNNlT9gIB90j6IPPSEIJSXCM04pPw97EFF1d4wP0BjvMsXau0hIWV09l40Oqlljb2d0V2ix0lW6w-mybZlJUof67y5mXgFIQWRzGb4fzb9uT2RULdMnuD_6os/s1600-h/whole-plot-SWG-MaxGlobal-Vs-SWG-PIDD.png"><img alt="whole-plot-SWG-MaxGlobal-Vs-SWG-PIDDensitySat[0.85]-large" border="0" height="480" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgomeePaM0C_KNczw89ODMP8kiSH0jX401useOnE10-qGRmOxfmoxTY-broi0IYfdSvLoFO889d2599-fSLezrBStC9bUZ3V0bliGvVbsd_o9m6i3tuyFxd7EWxSTwk7vE8OfbANL-KDFE/?imgmax=800" style="background-image: none; border-bottom-width: 0px; border-left-width: 0px; border-right-width: 0px; border-top-width: 0px; display: inline; padding-left: 0px; padding-right: 0px; padding-top: 0px;" title="whole-plot-SWG-MaxGlobal-Vs-SWG-PIDDensitySat[0.85]-large" width="480" /></a></td></tr>
<tr> <td valign="top" width="463"></td> <td valign="top" width="503"></td></tr>
<tr> <td valign="top" width="463"><ul> <ul>
<li><strong>MaxLocal Vs PID</strong></li>
</ul>
</ul>
</td> <td valign="top" width="503"><ul> <ul>
<li><strong>MinGlobal Vs PID</strong></li>
</ul>
</ul>
</td></tr>
<tr> <td valign="top" width="463"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEij8NtEqZFKxRMjYGkGPxgyhm1bqvrpheey18KSWCVyhU_TxeGggydezFQBHNQdkqpcO5GXc7gs6PEirJ2PX4oPRzvsJA6O0pxH1xQJpWQYcVCQpNqJALILznwTmSMqyyulE7LODeOYdPw/s1600-h/whole-plot-SWG-MaxLocal-Vs-SWG-PIDDe%25255B2%25255D.png"><img alt="whole-plot-SWG-MaxLocal-Vs-SWG-PIDDensitySat[0.85]-large" border="0" height="480" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhm9eznUEKrmNwE76nO7QhyGMX0UTImCMWvYa8eUivjTataOvSE0GTsQ2MmyMxaUlyha3vStFjoVyJJYqRyVZt6vH3miGkqgRRaHcd6WVxqbfk0gyQyioABrDNBWqKAELXt29J8E1um_vU/?imgmax=800" style="background-image: none; border-bottom-width: 0px; border-left-width: 0px; border-right-width: 0px; border-top-width: 0px; display: inline; padding-left: 0px; padding-right: 0px; padding-top: 0px;" title="whole-plot-SWG-MaxLocal-Vs-SWG-PIDDensitySat[0.85]-large" width="480" /></a></td> <td valign="top" width="503"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjWJAVc55hCiY4KEYSfYqJwwZeXv5fOxkHI65as3UqvtZSJ3RCNr6MpF4iUFWcAAYLbRHQsDeI-K6pZkQDOsTdODQLSyTPUJamH1bEAKH_NpO46IHeiiwwqtmCK6YpXAuwYygUwErhUAQ8/s1600-h/whole-plot-SWG-MinGlobal-Vs-SWG-PIDD%25255B1%25255D.png"><img alt="whole-plot-SWG-MinGlobal-Vs-SWG-PIDDensitySat[0.85]-large" border="0" height="480" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh3gUF7y1wM5WE4NP6Yw3EBWG5biBrXupPIPPAL3c-Dsx0a7Jitkb-HfJ47ThY2bGCLQRZPuO9JratA5yV0BzmMhuX8Rz5ihevQl9rBMqYnNn5jIiBaxQa5Mo9pnB5NjNn6gY7xXael5tY/?imgmax=800" style="background-image: none; border-bottom-width: 0px; border-left-width: 0px; border-right-width: 0px; border-top-width: 0px; display: inline; padding-left: 0px; padding-right: 0px; padding-top: 0px;" title="whole-plot-SWG-MinGlobal-Vs-SWG-PIDDensitySat[0.85]-large" width="480" /></a></td></tr>
<tr> <td valign="top" width="463"></td> <td valign="top" width="503"></td></tr>
<tr> <td valign="top" width="463"><ul> <ul>
<li><strong>MinLcal Vs PID</strong></li>
</ul>
</ul>
</td> <td valign="top" width="503"></td></tr>
<tr> <td valign="top" width="463"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjD6uxqsMbZWqFuL4OvKLO7spaBpDSIkthtTWIj_onLb8nS-_o6fLveg8WTFBuXPFOSxLsHZcY4PYrpVx3da52AiVN3AWEtW-0j0uL0r6_nKMAcgQ3EZLIsaCqq8OqOftrE6x3isv27wKI/s1600-h/whole-plot-SWG-MinLocal-Vs-SWG-PIDDe.png"><img alt="whole-plot-SWG-MinLocal-Vs-SWG-PIDDensitySat[0.85]-large" border="0" height="480" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj1zw_H4_DwquCzn3A1OtmH4aXaJ1CymqjSL1z4k1_DE5pYTA33OkgH4KSEXVKV0wvbf7e9bFPsdvt5klib7E4GHjttOU6OuIzh0ZCKllU0KrL_dauQ6ioMQuAIcHHRF1FwQaA2xQJe-8s/?imgmax=800" style="background-image: none; border-bottom-width: 0px; border-left-width: 0px; border-right-width: 0px; border-top-width: 0px; display: inline; padding-left: 0px; padding-right: 0px; padding-top: 0px;" title="whole-plot-SWG-MinLocal-Vs-SWG-PIDDensitySat[0.85]-large" width="480" /></a></td> <td valign="top" width="503"></td></tr>
</tbody></table>
<br />
<br />
<ul>
<li><span style="font-size: small;">Heatmaps of vs AvgLocal</span></li>
</ul>
<table border="0" cellpadding="2" cellspacing="0" style="width: 400px;"> <tbody>
<tr> <td valign="top" width="261"><ul> <ul>
<li><strong>MaxGlobal Vs AvgLocal</strong></li>
</ul>
</ul>
</td> <td valign="top" width="139"><ul> <ul>
<li><strong>MaxLocal Vs AvgLocal</strong></li>
</ul>
</ul>
</td></tr>
<tr> <td valign="top" width="261"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj2BMw-fFxAW8WOxlz00f6lvKVeC8cizz_KXdpCiYT1JLG3jlbZFzSGsGOYiDmWGzyA7IGduL9s6hs0s-1jOoupErrrYGcU83g8puBsehbXsAZfFAZ_5QKqnxfr7OYJOciKYOIXn7_H_hc/s1600-h/whole-plot-SWG-MaxGlobal-Vs-SWG-AvgL%25255B1%25255D.png"><img alt="whole-plot-SWG-MaxGlobal-Vs-SWG-AvgLocalDensitySat[0.85]-large" border="0" height="480" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgMtfXmgZdJrFJq7JliP4UXqeei7Rrdukr69oGaBgf79gWbWFBiOBginWgQkskf1e1dM0v-nKTEhRkop2ypIYhL5XAs_d7yb-Fic4nOuZX-sPuvxrm7uLVVgd0IeQyykryQ0uXYxIsm0Kk/?imgmax=800" style="background-image: none; border-bottom-width: 0px; border-left-width: 0px; border-right-width: 0px; border-top-width: 0px; display: inline; padding-left: 0px; padding-right: 0px; padding-top: 0px;" title="whole-plot-SWG-MaxGlobal-Vs-SWG-AvgLocalDensitySat[0.85]-large" width="480" /></a></td> <td valign="top" width="139"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjv2NcyLmlFQvPigtkN4F31DFQWMA55_m1GatxN-BOwsbzdLT5KMzs7yIZiyyIIAVxWJVFIApM2rQwlBIzpIU5goDypL0vLja8hVJBk13arjJyy574uKofG_SrOVaKDaS9F4gFPsANT7MY/s1600-h/whole-plot-SWG-MaxLocal-Vs-SWG-AvgLo%25255B1%25255D.png"><img alt="whole-plot-SWG-MaxLocal-Vs-SWG-AvgLocalDensitySat[0.85]-large" border="0" height="480" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjVGQRx_IIWV6t6TcBX9hTZhsgEppl7N4uA3tRjXbuUIQSf0ZoWc0-1qLezxPukyzJ2nugZORRsHbhwbHHon-epYFD2nEENprxgQRXDXY2aw7UhfE-SJ27xwfAH_D2hVnmz_CzVeFQNk_g/?imgmax=800" style="background-image: none; border-bottom-width: 0px; border-left-width: 0px; border-right-width: 0px; border-top-width: 0px; display: inline; padding-left: 0px; padding-right: 0px; padding-top: 0px;" title="whole-plot-SWG-MaxLocal-Vs-SWG-AvgLocalDensitySat[0.85]-large" width="480" /></a></td></tr>
<tr> <td valign="top" width="261"></td> <td valign="top" width="139"></td></tr>
<tr> <td valign="top" width="261"><ul> <ul>
<li><strong>MinGlobal Vs AvgLocal</strong></li>
</ul>
</ul>
</td> <td valign="top" width="139"><ul> <ul>
<li><strong>MinLocal Vs AvgLocal</strong></li>
</ul>
</ul>
</td></tr>
<tr> <td valign="top" width="261"></td> <td valign="top" width="139"></td></tr>
<tr> <td valign="top" width="261"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiNasyYl8VD5s3-MZUhFdQW1lydTzUQeEA4Mwvg-QUFRnejUONpjK5HaOGxXwBwpomW2FJxgX5bEgjDA_i5Yt8qCaKbFeu3HC1yfwt3vJ8FxdBYdvAT3pztsQMi1WZ0qtjqrDeTeDk6v0g/s1600-h/whole-plot-SWG-MinGlobal-Vs-SWG-AvgL.png"><img alt="whole-plot-SWG-MinGlobal-Vs-SWG-AvgLocalDensitySat[0.85]-large" border="0" height="480" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjJy1KCWb9ZBQ3S3E65mHh0KDNEwBRzgGF8kkNGsFyjK4rDS12fnLcnCiSfzGRgLi7uXo-i1pkgI-OypfY_GqQhoLryDSZxYyrRb1HEFClPDqYWYyPRYBie4NPQGgkjmHwUN5wc9TAVxiM/?imgmax=800" style="background-image: none; border-bottom-width: 0px; border-left-width: 0px; border-right-width: 0px; border-top-width: 0px; display: inline; padding-left: 0px; padding-right: 0px; padding-top: 0px;" title="whole-plot-SWG-MinGlobal-Vs-SWG-AvgLocalDensitySat[0.85]-large" width="480" /></a></td> <td valign="top" width="139"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEijkOQu_WOXmW3t3czENxQ4s9LvzsgksJxrQsIw_aNtps9KuLtpdxUl3zVuodSE8dAWPlnF6uk9njyuyhTS1KrSFO6r17XOLhvbMZycWs6xdHnQYfJutOC9N7rQZxR5-oD3alw6geLjO3s/s1600-h/whole-plot-SWG-MinLocal-Vs-SWG-AvgLo%25255B2%25255D.png"><img alt="whole-plot-SWG-MinLocal-Vs-SWG-AvgLocalDensitySat[0.85]-large" border="0" height="480" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjR4WLLZJhxM_fF1RV6mPKWOzyNiM3IN1kMRQYR2tl8jp-oHTsYgci-lnasg6Gheyg4szI0K7WkfPMppUBXZcOf4WmqtnxQMzxgWZKOrasBE7SNff-O2ICwgD4jR4WpWynJzX5MFtRv8vc/?imgmax=800" style="background-image: none; border-bottom-width: 0px; border-left-width: 0px; border-right-width: 0px; border-top-width: 0px; display: inline; padding-left: 0px; padding-right: 0px; padding-top: 0px;" title="whole-plot-SWG-MinLocal-Vs-SWG-AvgLocalDensitySat[0.85]-large" width="480" /></a></td></tr>
</tbody></table>
<br />
<ul>
<li><span style="font-size: small;">Heatmaps of vs MaxGlobal</span></li>
</ul>
<table border="0" cellpadding="2" cellspacing="0" style="width: 400px;"> <tbody>
<tr> <td valign="top" width="200"><ul> <ul>
<li><strong>MaxLocal Vs MaxGlobal</strong></li>
</ul>
</ul>
</td> <td valign="top" width="200"><ul> <ul>
<li><strong>MinGlobal Vs MaxGlobal</strong></li>
</ul>
</ul>
</td></tr>
<tr> <td valign="top" width="200"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgw7ccb082099L9bBWymA105mfndIFHyUART2zwzcF8ovg3P7K5i_j4PKRLrZKhBVBxVxCwV7SvEf04cYE7B9cLK6EB-U0aGKalqh8s2SMOEWDWwIU1eVVA4-_vP4vEbaCYHlEwzrVdkrI/s1600-h/whole-plot-SWG-MaxLocal-Vs-SWG-MaxGl.png"><img alt="whole-plot-SWG-MaxLocal-Vs-SWG-MaxGlobalDensitySat[0.85]-large" border="0" height="480" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjJHCQCD8ZAZevbbmZ5g2MPuH1RENOnH1iSvACGIdvcu0Bfa50coFFeNx4DeooMfaRMRWcGjdeRZ4-z5KX4eXIjSMnEFOoEoE9agPBqF6InCG7cwqDallNueQKSDIma45XSRyVcMXJkwgI/?imgmax=800" style="background-image: none; border-bottom-width: 0px; border-left-width: 0px; border-right-width: 0px; border-top-width: 0px; display: inline; padding-left: 0px; padding-right: 0px; padding-top: 0px;" title="whole-plot-SWG-MaxLocal-Vs-SWG-MaxGlobalDensitySat[0.85]-large" width="480" /></a></td> <td valign="top" width="200"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEguVKpWfDwmEivn4QFiNykbZ8lZzGKVm6BX981ZKvJMA9taT22C9q2YUyo8mULcOHF0A7pp9Y8QWncDVoMKtjaxuGtudbyF7Dht9Ll6yYKUC96v87GuMG1SzGdf6JDHGgBVs4CNjSf9L-c/s1600-h/whole-plot-SWG-MinGlobal-Vs-SWG-MaxG%25255B2%25255D.png"><img alt="whole-plot-SWG-MinGlobal-Vs-SWG-MaxGlobalDensitySat[0.85]-large" border="0" height="480" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi8AH5zai2UHe7MDBpul27Xv1EouhTj32Qh4TWrLGLD5dX0YsUJpt3yv3QM8T_rUTjnmiT95bjafqAeQxagqKVnFpO90DO2gdtPTjl6bUjLOvPvKSgUcNwWvFUhhJWhSZFIg0SNdjegY5k/?imgmax=800" style="background-image: none; border-bottom-width: 0px; border-left-width: 0px; border-right-width: 0px; border-top-width: 0px; display: inline; padding-left: 0px; padding-right: 0px; padding-top: 0px;" title="whole-plot-SWG-MinGlobal-Vs-SWG-MaxGlobalDensitySat[0.85]-large" width="480" /></a></td></tr>
<tr> <td valign="top" width="200"></td> <td valign="top" width="200"></td></tr>
<tr> <td valign="top" width="200"><ul> <ul>
<li><strong>MinLocal Vs MaxGlobal</strong></li>
</ul>
</ul>
</td> <td valign="top" width="200"></td></tr>
<tr> <td valign="top" width="200"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjzuEQwNcBmDs1s6LHA7wX0NXU2xIvRNbCxUZc8foQ8H0bi_Wm7v7lpmxK_1uXCzMx2EHgirDyn3cX7T5y09gYMvAmsz3skzcAQolAFNkHofitlGzPYHroavVat3848U2StiCvG1Ud_mNA/s1600-h/whole-plot-SWG-MinLocal-Vs-SWG-MaxGl.png"><img alt="whole-plot-SWG-MinLocal-Vs-SWG-MaxGlobalDensitySat[0.85]-large" border="0" height="480" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEin954e0SsUMiXeA4ua-eK2Z3A8nS3eVA5wlqrPranIrl3FM14dhl-kUJ5paJYtWL4wsi02nuOzN_vacCt33nsnyKsVV7kOb9KraJH16EAnYWrGUESlTGkQJjzBE8oFrcHZvkQk_P73H7Y/?imgmax=800" style="background-image: none; border-bottom-width: 0px; border-left-width: 0px; border-right-width: 0px; border-top-width: 0px; display: inline; padding-left: 0px; padding-right: 0px; padding-top: 0px;" title="whole-plot-SWG-MinLocal-Vs-SWG-MaxGlobalDensitySat[0.85]-large" width="480" /></a></td> <td valign="top" width="200"></td></tr>
</tbody></table>
<br />
<ul>
<li><span style="font-size: small;">Heatmaps of vs MaxLocal</span></li>
</ul>
<table border="0" cellpadding="2" cellspacing="0" style="width: 400px;"> <tbody>
<tr> <td valign="top" width="200"><ul> <ul>
<li><strong>MinGlobal Vs MaxLocal</strong></li>
</ul>
</ul>
</td> <td valign="top" width="200"><ul> <ul>
<li><strong>MinLocal Vs MaxLocal</strong></li>
</ul>
</ul>
</td></tr>
<tr> <td valign="top" width="200"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjI1Q-1gpihJ1IeJTGp2sU98HqUThCpNHI9ay6lvZhO8ZP-BlOidlB2-6ZJGHihl75SBhRVa3wUnKqiW1yqLKyVEujhOQcEHhrveylvYTd4hpD56DxCu4WHMECVD6pv7jH9yf_x4wJbntw/s1600-h/whole-plot-SWG-MinGlobal-Vs-SWG-MaxL%25255B2%25255D.png"><img alt="whole-plot-SWG-MinGlobal-Vs-SWG-MaxLocalDensitySat[0.85]-large" border="0" height="480" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgtfUApzT7zYQJJyAeQaRFVwIZH3Tv3c6WmCEBVuWmUIWx_9msN8KvDrbnlFPQVRqHZUZuTLUhFQvj4wHsQEjy6_dX7G89Gp8dJ2PdMl4o8bV5cGEVgI1DBCvSk_rjiLgE8EoptJaeRZuc/?imgmax=800" style="background-image: none; border-bottom-width: 0px; border-left-width: 0px; border-right-width: 0px; border-top-width: 0px; display: inline; padding-left: 0px; padding-right: 0px; padding-top: 0px;" title="whole-plot-SWG-MinGlobal-Vs-SWG-MaxLocalDensitySat[0.85]-large" width="480" /></a></td> <td valign="top" width="200"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg0OqGbBeoxHhlPPVWpZPsVQD8bBwSHwTmH5ljUn9LBEs6L0H2dSPeMMSOWbXdIQMBZFU3VjZ7V3R-RBOe3aruLLLbFRiSo6gry7PVlU_lFjRKZFlqOMWHiY50hBW71sQioEvY7dHiDM3Q/s1600-h/whole-plot-SWG-MinLocal-Vs-SWG-MaxLocalDensitySat%25255B0.85%25255D-large.png"><img alt="whole-plot-SWG-MinLocal-Vs-SWG-MaxLocalDensitySat[0.85]-large" border="0" height="475" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjEtR16tE_3xcSgS9K1EHH66ugr44Ya55Om3wrV0zpSKh5rrYH-uIIMe4L1Tg3EAztsDK6cuHYx3Fjyq2rH4jXRukBtge5sT2OLOJZ1B4HaaogpFlNgvaYV8XDrkN0gU9NO00o3nz0pkdM/?imgmax=800" style="background-image: none; border-bottom: 0px; border-left: 0px; border-right: 0px; border-top: 0px; display: inline; padding-left: 0px; padding-right: 0px; padding-top: 0px;" title="whole-plot-SWG-MinLocal-Vs-SWG-MaxLocalDensitySat[0.85]-large" width="480" /></a></td></tr>
</tbody></table>
<br />
<ul>
<li><span style="font-size: small;">Heatmaps of vs MinLocal</span></li>
</ul>
<table border="0" cellpadding="2" cellspacing="0" style="width: 400px;"> <tbody>
<tr> <td valign="top" width="200"><ul> <ul>
<li><strong>MinLocal Vs MinGlobal</strong></li>
</ul>
</ul>
</td> <td valign="top" width="200"></td></tr>
<tr> <td valign="top" width="200"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh5vxRVeMAuXvgCVJPYo35anQOOG7Wl4tI8Oz0TwcS9fG2yIjlHc98R3Rknrh2TwXfu2CTH9igvJWiTmnqhEWI42KkEzvUY4NvWNCzYKA3fIgArds9JznXGmqqFfg5j6_iar36PwD3s0Gk/s1600-h/whole-plot-SWG-MinLocal-Vs-SWG-MinGl%25255B1%25255D.png"><img alt="whole-plot-SWG-MinLocal-Vs-SWG-MinGlobalDensitySat[0.85]-large" border="0" height="480" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj1M1Kacsjd1PfYz7oxk90AX3WpTrICi0dVZsBix24Zzb-n2vf6JmWWWrmneMWdWhowWgcvKL3GpnnwEkNZ_cwA1qCFs3Mp_eHoHBpmhjKMRcT3TRvG6AGV6M2f56-i8jgAimoop2yExFc/?imgmax=800" style="background-image: none; border-bottom-width: 0px; border-left-width: 0px; border-right-width: 0px; border-top-width: 0px; display: inline; padding-left: 0px; padding-right: 0px; padding-top: 0px;" title="whole-plot-SWG-MinLocal-Vs-SWG-MinGlobalDensitySat[0.85]-large" width="480" /></a></td> <td valign="top" width="200"></td></tr>
</tbody></table>
Saliya Ekanayakehttp://www.blogger.com/profile/10281589417412608237noreply@blogger.com0tag:blogger.com,1999:blog-400445772342786430.post-10135374925663086822012-09-25T23:19:00.003-07:002014-08-24T13:23:16.009-07:00A study of Phylogenetic Tree generation in QIIME<h2>
<span style="background-color: white; font-family: Arial, Helvetica, sans-serif; font-size: 15px;">1. QIIME introduction</span></h2>
<span style="background-color: white; font-family: Arial, Helvetica, sans-serif; font-size: 15px;">QIIME stands for <b>Quantitative Insights Into Microbial Ecology</b>. It takes input as raw sequencing files (usually FASTA files) and output initial analyses such as OTU picking, taxonomic assignment, and as well as construction of phylogenetic trees from representative sequences of OTUs. It also provide downstream statistical analysis, visualization, and production of publication-quality graphics.</span><br />
<span style="background-color: white; font-family: Arial, Helvetica, sans-serif; font-size: 15px;"><br /></span>
<br />
<h2>
<span style="font-family: Arial, Helvetica, sans-serif; font-size: 15px;">2. QIIME pipeline</span></h2>
<span style="font-family: Arial, Helvetica, sans-serif;">Currently, our pipeline, DACIDR includes:</span><br />
<b><span style="font-family: Arial, Helvetica, sans-serif;">Pairwise Sequence Alignment (PSA) -> Deterministic Annealing Pairwise Clustering (DA-PWC) / Multidimensional Scaling (MDS) -> Region Refinement -> Interpolation -> Generate OTUs -> Select Center Sequence (Reference Sequences) -> <i>Generate Phylo Tree</i></span></b><br />
<span style="font-family: Arial, Helvetica, sans-serif;">And Qiime includes:</span><br />
<span style="font-family: Arial, Helvetica, sans-serif;"><b>Clustering (Picking OTUs) -> Choosing Reference Sequence</b> -> <i><b>Multiple Sequence Alignment -> Alignment Filter (Removing Unnecessary Gaps) -> Build Phylo Tree</b></i> -> <strike>Build an OTU table</strike></span><br />
<div style="text-align: justify;">
<span style="font-family: Arial, Helvetica, sans-serif; line-height: 20px;">The Clustering step in QIIME has very similar function in DACIDR, where both of them input the FASTA files and output clustering result with reference sequences. QIIME clustering choices are usearch, usearch_ref, prefix_suffix, mothur, trie, blast, uclust_ref, cdhit and uclust. The reference sequence is usually selected as most abundant sequence.</span></div>
<div style="text-align: justify;">
<span style="font-family: Arial, Helvetica, sans-serif; line-height: 20px;">However, in QIIME, they have more steps to generate the Phylogenetic Tree, where the details are present below:</span><br />
<span style="font-family: Arial, Helvetica, sans-serif; line-height: 20px;"><br /></span></div>
<div style="text-align: justify;">
<h3>
<span style="font-family: Arial, Helvetica, sans-serif; line-height: 20px;">2. 1 Multiple Sequence Alignment</span></h3>
</div>
<div style="text-align: justify;">
<span style="font-family: Arial, Helvetica, sans-serif; line-height: 20px;"></span></div>
<span style="font-family: Arial, Helvetica, sans-serif;">The QIIME has three choice of multiple sequence alignment: <a href="http://pynast.sourceforge.net/">PyNAST</a>(Caporaso et al., 2009),<a href="http://www.ebi.ac.uk/Tools/msa/muscle/"> </a><span style="background-color: white;"><a href="http://www.ebi.ac.uk/Tools/msa/muscle/">MUSCLE</a>(</span><span style="background-color: white;">Edgar, 2004) and </span><a href="http://infernal.janelia.org/">INFERNAL</a> (Nawrocki, Kolbe, & Eddy, 2009).</span><br />
<span style="font-family: Arial, Helvetica, sans-serif; line-height: 20px;">PyNAST is a python implementation of the NAST alignment algorithm. The NAST algorithm aligns each provided sequence (the “candidate” sequence) to the <i>best-matching sequence in a pre-aligned database of sequences</i> (the “template” sequence). Candidate sequences are not permitted to introduce new gap characters into the template database, so the algorithm introduces local mis-alignments to preserve the existing template sequence, <b>which means if we want to use PyNAST, we need to have to a template of sequences which looks like:</b><br />
</span><br />
<div style="border: 1px solid rgb(153, 153, 153); height: 200px; overflow: auto; text-align: left; width: 600px;">
<span style="font-family: Arial, Helvetica, sans-serif; line-height: 20px;">>114239 </span><br />
<span style="font-family: Arial, Helvetica, sans-serif; line-height: 20px;">............................................................................................................aGAGTTT-GA--T-CC-T-G-GCTC-AG-AT-TGAA-C-GC--TGG-C--G-GT-A-TG--C----T-T--AACACA-T-GC-A-AGT-CGA-A-CG----------G-TAA-CA-G-----------------------------CAG-A-AG----------------------------------------------------CTT-G----------------------------------------------------------------------------------CTT-CT------------------GGCT--G--AC--G--AG-T-GG-C-GG-A--C-------------GGG-TGAGT-A--AC-GC-G-T-A-GG---A-A--T-CT-G--C-CTTA---CA-G------------------------------------------------------------------T-GG----GGG-AT-AG-CCC-------------------------G-G-T-----------------------GAA-A---ACC-GGA-TTAA-TA---CC-G--C-AT-A----------C--------------------G-------------------------------------CC-C-----------------------------------------------------------------------------------------------------------------------T-AC-G--------------------------------------------------------------------------------------------------------------------------------------G-G-G---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAAA--G-CTG--G-----G--GA-T--C--------------------------------------------------------------------------------------------------------------------TTC-G----------------------------------------------------------------------------------------------------------------------G-A--CC-TG--G---C-A--------------C----T-G---T-TA-G---AT---G-A-----G-CCT-GCG--T-GAG--A------TT--A--G-CT-T----G---TTGG-T-G-GG-G-T----AAT-GG---C-CTACCA--A-GG-C-A--A-CG-A------------TCT-C-T------AG-CT-G-G-TCT-G-AG----A--GG-AC--G-AT-C-AG-CCAC-A-CTGGG--A-C-TG-A-GA-C-AC-G-GCCCAG-A-CTCC-TAC-G--G-G-A-G-GC-A-GC-A-G-TG---GG-G-A-ATA-TTGCA-C-AA-T-GG--GC-GA-G----A-G-CC-T-GA-TG-CA-GCAA-TACC-G-CG-T---G-T-G--T--GA-A-G--A--A-G-G--C----CTG-AG---------G-G-T-T-G-T--A---AA-G-CAC--------TT-TC-A-A--T--TG---TGA-A--G---AAAAGCT---T-TT-GG----T--T--AA-T---A----------AC-C-TTGAGTC-TT-GA-CA-TTAA-C-A--A-TA-C---------AA-----------GAAGC-ACC-GG-C-TAA---C--T-CCGT--GCCA--G-C---A--GCCG---C-GG--TA-AT--AC---GG-AG-GGT-GCA-A-G-CG-TTAA-T-CGG-AA-TT-A--C-T--GGGC-GTA----AA-GAGT-AC--G-TA-G-G-T-G------------G--T-TC-G-T-T-AA----GTC---A---G-ATG-TG-A-AA-GC--CC-CGG-G--------------------------------------------------------------------CT-C-AA-------------------------------------------------------------------------CC-T-G-GG-AA-C----T-G-C-A-T-T--------T---GAA-A-C-T-G-GCA--A-A-C---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T-T-G-A-G-T-A-----T-GG--TA-G-A------------G-GC-G-GG-T----AG--AA-T-TCA-TAGT--GT-A-GCG-GTGAAA-TG-CGT-AGAT-ATTA-T-G-A--GG-A-AT-A-CC-AG--T--G--GC-GAA-G--G-C---G----G--C-C-CGCTG------G-AC-CA--------------------------------------------------------------AT-A-C-C--GA--CA-----CT-GA-GG--T-A-CGA--AA-G-C--------------G-TGGG-GAG-C-G-AACA--GG-ATTA-G-ATA-C-----CC-T-G-GTA-G-T----C-CA--C-G-CCG-T-AAA--C-GATG-TC--AA-CT---------A-GC--C--G-T-TG-G-GA-C-----------------------------------------------------------------------------------------CTT-GA--------------------------------------------------------------------------------------------------------------------------------------------------G-G-T-CT--C-A-G-T-GG-T------GC--A----GC-TAA--CG-C---G--T-GAA-GT--T----G-ACC-GCC-T-G-GG-GAG-TA---CGG-----C-C--G-C-A-A-GGC-T--AAA-ACTC-AAA---------TGAA-TTG-ACGAG-G-G-CCCG----C-A--C-A-A-GCG-GT-G--G--AG-CA-T--GT-GGT-TT-AATT-C-G-ATG-CAAC-G-CG-A-AG-A-A-CC-TT-A-CC-ATCCC-TT-G-AC-ATC-A---------------TC-A-G-------------A-A--CTT-G--TT--A-GA-G-A-T--A-A-C----T-CGG--T-G-----CC-------------------------------------T--TC-G------------------------------------------GG------------AA--CTGA-AT--GA---------------------------------------------------C-A-G-G-T-GCTG-CA-TGG-CT--GTC-GTC-A-GC-TC---G-TG-TC-G--TGA-GA-TGT-T-GG-G-TT-AA-GT-CCCGC-AA--------C-GAG-CGC-A-ACC-C-T-TA--TC--C-TTAG--T-T-G-C-C---AG-C-A----CG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAAT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GG---T----G-G-----------------G---A-A--CT---------------C-T-A-A-G-GA-G--AC-T-G-CCG--G-T------------------------------------G-A---TAA----------------------------------A-C-C-G--G-A-GG-A--AGG-T--GGGG-A-TGAC-GTC--AAGT-C---ATC-A-T-G-G-C-C-CTT----AT-G--GG-A-T-GG-GC-TA-CAC-ACGTG-C--TA--CAATG---G-T-CA-GTA--C-AAA-GG-GC--------------------------------------------------------------------------------------------------A-G-C-C-A--A-CTCG-C--G---------------------------------------A-GA-G-T-----------G--C-G-CA---A----------A--TCC-C------A-T-AAAGCTGA---T-C-G-TAG-TCC--------GGA-T-TGGAG-TC--T-GCAA-CT-C-------------------------------------------------------------------------------------------------G-ACTCC-A-T-G-AA-G-TT-GGAAT-CG-C-TA--G-TA-AT-C-G-T----GAA-TC-A-G--A------AT--GTC-AC-G-GT-G-AAT-ACGT-T-CCCGGGCCT-TGCA----CACACCG-CCC-GTC-----a---ca--cca-tg-gg-a--g---tgg-g-ct-gc-aaa--a-gaa------g--t-agg-ta-g-t-t-t-aa-c-c--------------------------------------------------------------ttc-g------------------------------------------------------------------------------------------------------gg-a--ga-a--c---gc-tta--cc--act-t----t-gtg-gt-tca------------------------tg--act-gggg-tg-aag-tcgtaacaa-ggtag-ccct-aggggaa-cctg-gggc-tggatcacctcctt.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
</span></div>
<span style="font-family: Arial, Helvetica, sans-serif;"><span style="line-height: 20px;">MUSCLE is an alignment method which stands for MUltiple Sequence Comparison by Log-Expectation. We can directly use MUSCLE for multiple sequence alignment, where I used this to play around a very small set of sequences. <b>However, MUSCLE is slower than PyNAST when sequence number is large.</b><br />Infernal (“INFERence of RNA ALignment”) is for an alignment method for using RNA structure and sequence similarities.</span><span style="line-height: 20px;">Infernal takes a multiple sequence alignment with a corresponding secondary structure annotation. <b>This input file must be in Stockholm alignment format. It requires a template of sequence and performs the slowest out of these 3 methods.</b></span></span><br />
<span style="font-family: Arial, Helvetica, sans-serif;"><span style="line-height: 20px;"><b><br /></b></span></span>
<br />
<div>
<h3>
<span style="font-family: Arial, Helvetica, sans-serif; line-height: 20px;"><b>2.2 Alignment Filter</b></span></h3>
</div>
<div>
<span style="font-family: Arial, Helvetica, sans-serif; line-height: 20px;">This component is used to remove positions which are gaps in every sequence. Additionally, the user can supply a <i>lanemask</i> file, that defines which positions should included when building the tree, and which should be ignored. A lanemast file looks like this:</span></div>
<div style="border: 1px solid rgb(153, 153, 153); height: 200px; overflow: auto; text-align: left; width: 600px;">
<span style="font-family: Arial, Helvetica, sans-serif;">000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001101111010110011101001011010110010000101001111110101101011101110101110000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000110101101011010010000000000000111011111010011011010101011000111001011010010101110011010000000000000000000000000000000000000000000000000000000000000000001011000011101101101110000000000000000000000000101010000000000000000000000011101000111011101111011000110100101101000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001000010100010110100011000101000001011101110010111001000000110010010110100001000111101010110101000011101101010101111001011010100101101000000000000111010100000011011010101110
</span></div>
<span style="font-family: Arial, Helvetica, sans-serif;"><br /></span>
<br />
<h3>
<span style="font-family: Arial, Helvetica, sans-serif;">2.3 Generate Phylogenetic Tree</span></h3>
<span style="font-family: Arial, Helvetica, sans-serif;">After the multiple sequence alignment is done on the reference sequence set, the phylogenetic tree can be produced. The methods provided in QIIME includes clearcut, clustalw, raxml, fasttree_v1, fasttree, raxml_v730 and muscle. <b>The default setting is to use FastTree (Price, Dehal, & Arkin, 2009), which takes only a few seconds to generate a tree with around 200 sequences in my test.</b></span><br />
<span style="font-family: Arial, Helvetica, sans-serif;"><b><br /></b></span>
<div>
Reference:</div>
<div>
<li style="font-family: TrebuchetMS, Arial, sans-serif; font-size: 13px; line-height: 16.79599952697754px; list-style: circle; margin-left: 30px; margin-top: 10px;">Yang Ruan, Geoffrey House, Saliya Ekanayake, Ursel Schütte, James D. Bever, Haixu Tang, Geoffrey Fox. <a href="http://salsahpc.indiana.edu/millionseq/reference/Integration%20of%20Clustering%20and%20Multidimensional%20Scaling%20to%20Determine%20Phylogenetic%20Trees%20as%20Spherical%20Phylograms%20Visualized%20in%203%20Dimensions.pdf" style="background-attachment: inherit; background-clip: inherit; background-image: inherit; background-origin: inherit; background-position: inherit; background-repeat: inherit; background-size: inherit; color: #0066b3; text-decoration: none;">Integration of Clustering and Multidimensional Scaling to Determine Phylogenetic Trees as Spherical Phylograms Visualized in 3 Dimensions.</a> Proceedings of C4Bio 2014 of IEEE/ACM CCGrid 2014, Chicago, USA, May 26-29, 2014.</li>
<li style="font-family: TrebuchetMS, Arial, sans-serif; font-size: 13px; line-height: 16.79599952697754px; list-style: circle; margin-left: 30px; margin-top: 10px;">Yang Ruan, Geoffrey Fox. <a href="http://salsahpc.indiana.edu/millionseq/reference/WDA-SMACOF_v1.02.pdf" style="background-attachment: inherit; background-clip: inherit; background-image: inherit; background-origin: inherit; background-position: inherit; background-repeat: inherit; background-size: inherit; color: #0066b3; text-decoration: none;">A Robust and Scalable Solution for Interpolative Multidimensional Scaling with Weighting.</a> Proceedings of IEEE eScience 2013, Beijing, China, Oct. 22-Oct. 25, 2013. (Best Student Innovation Award)</li>
<li style="font-family: TrebuchetMS, Arial, sans-serif; font-size: 13px; line-height: 16.79599952697754px; list-style: circle; margin-left: 30px; margin-top: 10px;">Yang Ruan, Saliya Ekanayake, Mina Rho, Haixu Tang, Seung-Hee Bae, Judy Qiu, Geoffrey Fox. <a href="http://salsahpc.indiana.edu/millionseq/reference/DACIDR_camera_ready_v0.3.pdf" style="background-attachment: inherit; background-clip: inherit; background-image: inherit; background-origin: inherit; background-position: inherit; background-repeat: inherit; background-size: inherit; color: #0066b3; text-decoration: none;">DACIDR: Deterministic Annealed Clustering with Interpolative Dimension Reduction using a Large Collection of 16S rRNA Sequences.</a> Proceedings of ACM-BCB 2012, Orlando, Florida, ACM, Oct. 7-Oct. 10, 2012.</li>
<li style="font-family: TrebuchetMS, Arial, sans-serif; font-size: 13px; line-height: 16.79599952697754px; list-style: circle; margin-left: 30px; margin-top: 10px;">Yang Ruan, Zhenhua Guo, Yuduo Zhou, Judy Qiu, Geoffrey Fox. <a href="http://salsahpc.indiana.edu/millionseq/reference/HyMR_submission_HPDC_workshop_final.pdf" style="background-attachment: inherit; background-clip: inherit; background-image: inherit; background-origin: inherit; background-position: inherit; background-repeat: inherit; background-size: inherit; color: #0066b3; text-decoration: none;">HyMR: a Hybrid MapReduce Workflow System.</a> Proceedings of ECMLS’12 of ACM HPDC 2012, Delft, Netherlands, ACM, Jun. 18-Jun. 22, 2012</li>
<li style="font-family: TrebuchetMS, Arial, sans-serif; font-size: 13px; line-height: 16.79599952697754px; list-style: circle; margin-left: 30px; margin-top: 10px;">Adam Hughes, Yang Ruan, Saliya Ekanayake, Seung-Hee Bae, Qunfeng Dong, Mina Rho, Judy Qiu, Geoffrey Fox. <a href="http://www.biomedcentral.com/1471-2105/13/S2/S9" style="background-attachment: inherit; background-clip: inherit; background-image: inherit; background-origin: inherit; background-position: inherit; background-repeat: inherit; background-size: inherit; color: #0066b3; text-decoration: none;">Interpolative Multidimensional Scaling Techniques for the Identification of Clusters in Very Large Sequence Sets</a>, BMC Bioinformatics 2012, 13(Suppl 2):S9.</li>
</div>
Anonymoushttp://www.blogger.com/profile/12376883776057140162noreply@blogger.com0tag:blogger.com,1999:blog-400445772342786430.post-52875623264879124762012-09-24T18:21:00.003-07:002012-09-24T18:49:25.335-07:00Phy Tree on Side Plot<br />
<h3>
Description</h3>
Environment: Tempest; 32 nodes (768 cores)<br />
Aligner: SmithWaterman<br />
ScoringMatrix: EDNAFULL<br />
GapOpen: -16<br />
GapExt: -4<br />
DistanceType: (1-Normalized Score*), Percentage Identity<br />
Method: 1291+123+74+420 all varied<br />
WithReverse: dynamic determine algorithm<br />
<h3>
Dataset</h3>
1) 1291 new GenBank sequences; (id:617~1907)<br />
2) 123 consensus sequence; (id: 420~542)<br />
3) 74 sequences from Gen Bank; (id: 543~616)<br />
4) 420 center sequences; (id: 0~419)
<br />
<br />
<h3>
<b>Tree Configuration</b></h3>
<div style="border: 1px solid rgb(153, 153, 153); height: 200px; overflow: auto; text-align: left; width: 600px;">
<pre>New sequences from Gen Bank: Hexagon
Consensus sequence in Haixu 123: Triangle
Center sequences in 420: original points
Root: Sphere
</pre>
<pre>Color Scheme: <span style="text-align: -webkit-auto;"> 1) Phylogenetic tree generated </span><a href="http://salsahpc.indiana.edu/PhylogeneticTree/197_new_tree_coloring.pdf">here</a></pre>
<pre> 2) Mega Region coloring</pre>
</div>
<br />
<h3>
Final Result</h3>
<h4>
Phylogenetic tree coloring:</h4>
1. <a href="http://salsahpc.indiana.edu/PhylogeneticTree/1908_pid_manxcat_z.pviz">Plot File</a> in PVIZ format, with pid distance.<br />
2. <a href="http://salsahpc.indiana.edu/PhylogeneticTree/1908_normalizedScore_manxcat_z.pviz">Plot File</a> in PVIZ format, with old* score distance.<br />
<h4>
Mega Region coloring:</h4>
3. <a href="http://salsahpc.indiana.edu/PhylogeneticTree/1908_normalizedScore_manxcat_z_megaRegion-color.pviz">Plot File</a> in PVIZ format, with old* score distance.<br />
<h4>
Screen Shot
</h4>
<div>
1. pid distance</div>
<div class="separator" style="clear: both; text-align: center;">
</div>
<div>
<div class="separator" style="clear: both; text-align: center;">
<img border="0" height="283" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgXzxkuUBy4Hk_iKW_BFZZFQwWbtZXRVipB3cP9xbvmR22o3Y44-88RqhUZkasOTG3bubN-Hmy97AiTXoLc_W6FjZ56W6fAJdGYW7Gg9kxz0lOiywuuHOFiD-maNblm0F7022qz40SIfy2K/s320/1908_pid_manxcat_z.png" width="320" /></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: left;">
2. old* score distance</div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhvTj8pYjt0apIrLBDhIauelYwTIvPp7KMq0Cnkazu1EswBQK_K9h-tZ3fRV3CGIfsDjwz6lGPzeNlFKjbV5MZekXmLqbnd0jAeuvW02FZtVn5u3suRESK50JOXhs-LihwcUWdklSWlo20i/s1600/1908_normalizedScore_manxcat_z.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="283" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhvTj8pYjt0apIrLBDhIauelYwTIvPp7KMq0Cnkazu1EswBQK_K9h-tZ3fRV3CGIfsDjwz6lGPzeNlFKjbV5MZekXmLqbnd0jAeuvW02FZtVn5u3suRESK50JOXhs-LihwcUWdklSWlo20i/s320/1908_normalizedScore_manxcat_z.png" width="320" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
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3. old* score distance with mega region</div>
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<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEihGktP6nOLjmlSD5gATLWuM1MVnYzXcoPK4TnTVGy4r2vtrmE1g2KJ1N3IxkHmoAJt0HcXBt9advB4d6OWu9IWn0lvSBLRyCHouP8ewHSl2F3z4_JG9qh6gLRQsSqadid_VmkHW8YvNIUN/s1600/1908_normalizedScore_manxcat_z_megaRegion-color.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="283" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEihGktP6nOLjmlSD5gATLWuM1MVnYzXcoPK4TnTVGy4r2vtrmE1g2KJ1N3IxkHmoAJt0HcXBt9advB4d6OWu9IWn0lvSBLRyCHouP8ewHSl2F3z4_JG9qh6gLRQsSqadid_VmkHW8YvNIUN/s320/1908_normalizedScore_manxcat_z_megaRegion-color.png" width="320" /></a></div>
<br /></div>
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</div>
Anonymoushttp://www.blogger.com/profile/12376883776057140162noreply@blogger.com0tag:blogger.com,1999:blog-400445772342786430.post-50493799402500163092012-04-20T10:40:00.000-07:002012-04-20T10:40:52.699-07:00PhyTree visualized on 123+74+420+100k (pid distance)<br />
<h4>
Description</h4>
Environment: Tempest; 32 nodes (768 cores)<br />
Aligner: SmithWaterman<br />
ScoringMatrix: EDNAFULL<br />
GapOpen: -16<br />
GapExt: -4<br />
DistanceType: (1-Normalized Score)<br />
Method: 100k+123 fixed, 74 and 420 varied<br />
WithReverse: 74 reversed, 420 not reversed
<br />
<h4>
Dataset</h4>
1) 100k selected from 440k; (id:617~100616)<br />
2) 123 consensus sequence; (id: 420~542)<br />
3) 74 sequences from Gen Bank; (id: 543~616)<br />
4) 420 center sequences; (id: 0~419)
<br />
<br />
<b>Tree Configuration</b><br />
<div style="border: 1px solid rgb(153, 153, 153); height: 200px; overflow: auto; text-align: left; width: 600px;">
<pre>New sequences from Gen Bank: Hexagon
Consensus sequence in Haixu 123: Triangle
Center sequences in 420: Rectangle
Root: Sphere
</pre>
<pre>Color Scheme: <span style="text-align: -webkit-auto;"> Phylogenetic tree generated </span><a href="http://salsahpc.indiana.edu/PhylogeneticTree/cluconsRplus20111127m-MLGTRG5UA100.pdf" style="text-align: -webkit-auto;">here</a></pre>
</div>
<br />
<h4>
Final Result</h4>
1. All shown <a href="http://salsahpc.indiana.edu/PhylogeneticTree/SIMPLEpoints_grouped_labeled_color_all_420.pviz">Plot File</a> in PVIZ format <br />
<h4>
Screen Shot
</h4>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgLSBd5RgwuPNsRnjJIWuURrdu2vuuc2oTItOfZMXWrYbsoo0z2rDrG4FGvfTM-71deEt6KRA5qlS7qYGE8WMlqeIgzFl0jgt_Er0y5jTqAvslHnK6gE3pk3-Fu7hfatVXSPjeCs2oQh8LT/s1600/SIMPLEpoints_grouped_labeled_color_all_420.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="252" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgLSBd5RgwuPNsRnjJIWuURrdu2vuuc2oTItOfZMXWrYbsoo0z2rDrG4FGvfTM-71deEt6KRA5qlS7qYGE8WMlqeIgzFl0jgt_Er0y5jTqAvslHnK6gE3pk3-Fu7hfatVXSPjeCs2oQh8LT/s400/SIMPLEpoints_grouped_labeled_color_all_420.png" width="400" /></a></div>
<div>
<br /></div>
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</div>Anonymoushttp://www.blogger.com/profile/12376883776057140162noreply@blogger.com0tag:blogger.com,1999:blog-400445772342786430.post-71709538040164328552012-04-12T22:03:00.004-07:002012-04-12T22:03:54.023-07:00PhyTree visualized on 197 (pid and score distance)<h4>
Input</h4>
1) PID distance<br />
Aligner: SmithWaterman<br />
ScoringMatrix: EDNAFULL<br />
GapOpen: -16<br />
GapExt: -4<br />
DistanceType: (1-PercentIdentity)<br />
WithReverse: Yes<br />
<br />
2) Score distance<br />
Aligner: SmithWaterman<br />
ScoringMatrix: EDNAFULL<br />
GapOpen: -16<br />
GapExt: -4<br />
DistanceType: (1-Normalized Score)<br />
WithReverse: Yes<br />
<br />
<h4>
Visualization Algorithm </h4>
DA-SMACOF
<br />
<h4>
Result in Plot</h4>
<div>
1) <a href="http://salsahpc.indiana.edu/PhylogeneticTree/197_pid_smacof_label_colored.pviz">Plot</a> from PID distance</div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjiEreSOGUFhXT9fR-6QC6JVw7Yms4ncn5mu_iFR6-2sEXPbUagGzFBQRDgMOWsoQMLttBKH_Y60O8GoHC_BdSQ2o6g3QDrWGGcr2FX6fWNF3X0xjxed6zlS9RqmvBR6DM1eG_C1BrrpEdu/s1600/197_pid_smacof_label_colored.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="353" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjiEreSOGUFhXT9fR-6QC6JVw7Yms4ncn5mu_iFR6-2sEXPbUagGzFBQRDgMOWsoQMLttBKH_Y60O8GoHC_BdSQ2o6g3QDrWGGcr2FX6fWNF3X0xjxed6zlS9RqmvBR6DM1eG_C1BrrpEdu/s400/197_pid_smacof_label_colored.png" width="400" /></a></div>
<div>
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
</div>
<div>
<br /></div>
<div>
2) <a href="http://salsahpc.indiana.edu/PhylogeneticTree/197_score_smacof_label_colored.pviz">Plot</a> from Score distance</div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgjtc1g8cDOS0l7a3ZHEEYV41t7u02JH4CUrpJ1xAmeS5BC3ppfP2d5eE64bqshoQ0-4_2TCI2Et2J1Fi8g6s-92JJ9V5_D0hAM2VmVtyyHLdqlxgBZa4HfTTJ_k_lUvumfv19Sz_YMYlEM/s1600/197_score_smacof_label_colored.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="353" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgjtc1g8cDOS0l7a3ZHEEYV41t7u02JH4CUrpJ1xAmeS5BC3ppfP2d5eE64bqshoQ0-4_2TCI2Et2J1Fi8g6s-92JJ9V5_D0hAM2VmVtyyHLdqlxgBZa4HfTTJ_k_lUvumfv19Sz_YMYlEM/s400/197_score_smacof_label_colored.png" width="400" /></a></div>
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<br /></div>Anonymoushttp://www.blogger.com/profile/12376883776057140162noreply@blogger.com0tag:blogger.com,1999:blog-400445772342786430.post-83575232362475387882012-04-12T17:40:00.000-07:002012-04-12T19:17:48.639-07:00Detailed Analysis on Length Effect<h4>
Input</h4>
8 sequences selected from 100k+197+420 FASTA file<br />
<br />
<h4>
Description</h4>
Aligner: SmithWaterman<br />
OpenGapPentalty: -16<br />
GapExtensionPenalty: -4<br />
WithReverseCompliment: No<br />
<h4>
Configuration</h4>
<br />
<div style="border: 1px solid rgb(153, 153, 153); height: 200px; overflow: auto; text-align: left; width: 600px;">
<pre><b><i>Sequence IDs:</i></b></pre>
<pre>73394
48231
20081
53373
81334
20764
25672
76209
</pre>
</div>
<h4>
Result</h4>
<b>1) Self aligned Result
</b><br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjV8W8SF9cg_Rbas8g6DJD_0HoKKK0JXe2afZ-zHgIu8M6sAna0n_IiXjgAFhe5LvhnY0rYrsWPlRUo3yqHY0U6FOsx6UoKPavfgSomVZJZDlnjSG_0meACZqQr85vcE34D4J04OMc7gxZ9/s1600/Analysis_based_on_self_alignment.PNG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjV8W8SF9cg_Rbas8g6DJD_0HoKKK0JXe2afZ-zHgIu8M6sAna0n_IiXjgAFhe5LvhnY0rYrsWPlRUo3yqHY0U6FOsx6UoKPavfgSomVZJZDlnjSG_0meACZqQr85vcE34D4J04OMc7gxZ9/s1600/Analysis_based_on_self_alignment.PNG" /></a></div>
<br />
<br />
<b>2) Aligned Result based on analysis on 73394
</b><br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjMKsHw9PjhmQIrwBzUOSQteLoXXxF2dekL_nJmcrsR_-POOR8_u8S7tt3kwOSufI6ekb7LEMQ611elzdKmF49ZW-RQ3XA7Ki44FfU_h02QfmB1iNq3E_AEfxHs93sxDCFhyphenhyphenvVP646KLOdW/s1600/Analysis_based_on_73394.PNG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjMKsHw9PjhmQIrwBzUOSQteLoXXxF2dekL_nJmcrsR_-POOR8_u8S7tt3kwOSufI6ekb7LEMQ611elzdKmF49ZW-RQ3XA7Ki44FfU_h02QfmB1iNq3E_AEfxHs93sxDCFhyphenhyphenvVP646KLOdW/s1600/Analysis_based_on_73394.PNG" /></a></div>
<b><br /></b><br />
<b>3) Distance Result based on 73394(id) sequence</b><br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhUxKGGLfY0wZtLJpTJb8KDbhZeYh8DLresUomdAlnSJOBNdAsDwDufKECh3mCaTLuVR1LrgedahVZ29pvi0zHoYZOY-DcwWp0T4a2PS19HhxVZk1zQgseKCYni5xvKPgeJvzL_ZeBVbmyK/s1600/Analysis_distance.PNG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhUxKGGLfY0wZtLJpTJb8KDbhZeYh8DLresUomdAlnSJOBNdAsDwDufKECh3mCaTLuVR1LrgedahVZ29pvi0zHoYZOY-DcwWp0T4a2PS19HhxVZk1zQgseKCYni5xvKPgeJvzL_ZeBVbmyK/s1600/Analysis_distance.PNG" /></a></div>Anonymoushttp://www.blogger.com/profile/12376883776057140162noreply@blogger.com0