GSF R1/R2 Data: Heatmaps for (R1/R2) + "Master" Data - 2

• R1 100K + Master 1020 SWG PID Vs. Alignment Length

• Reversed R2 100K + Master 1020 SWG PID Vs. Alignment Length

GSF R1/R2 Data: Histograms for (R1/R2) + "Master" Data

• SWG Alignment Lengths

• SWG PID

GSF R1/R2 Data: Heatmaps for (R1/R2) + "Master" Data

• 100K+1020 R1 Reversed Alignment Length Vs Alignment Length

• 100K+1020 R1 Reversed Score Vs Score

• 100K+1020 R2 Reversed Alignment Length Vs Alignment Length

• 100K+1020 R2 Reversed Score Vs Score

GSF R1/R2 Data: Heatmaps for (R1/R2) Data

Heatmaps for corresponding 100k random samples of GSF data.

• R2 SWG PID Vs R1 SWG PID

• R1 SWG PID Vs R1 SWG Align Length -- length cut > 100 on right

• R2 SWG PID Vs R2 SWG Align Length -- length cut > 100 on right

revised 599nts and 999nts Raxml vs Clustering using Spherical Phylogenetic Tree

Dataset

1. revised 599nts
This work follows the previous work on http://salsafungiphy.blogspot.com/2013/09/pairwise-distances-from-msa-vs-pairwise.html
This dataset has a total number of 831 sequences.
2. 999nts
This work follows the previous work on http://salsafungiphy.blogspot.com/2013/06/pairwise-distances-from-multiple.html
This dataset has a total number of 1306 sequences.

Alignment

The clustering was done based on
1) SWG, using EDNAFULL scoring matrix, with gap open = -16 and gap extension = -4
2) Multiple sequence alignment, PID.

The Raxml was done based on multiple sequence alignment,
1) revised 599nts, newick file
2) 999nts, newwick file

Spherical Tree

The information of spherical tree can be found on previous work of http://salsafungiphy.blogspot.com/2012/11/phylogenetic-tree-generation-for.html and http://salsafungiphy.blogspot.com/2012/11/phylogenetic-tree-mega-table.html

Dimension Reduction

Manxcat SMACOF:
The pviz file for SWG clustering result with revised 599nts is here, for 999nts is here.
For MSA clustering result with revised 599nts is here, for 999nts is here.
WDA-SMACOF:
alpha set to 0.95
The pviz file for SWG clustering result with revised 599nts is here, for 999nts is here.
For MSA clustering result with revised 599nts is here, for 999nts is here.

Sum of branch lengths (edge sum)

(note that the difference of edge sum between SWG and MSA should due to the difference of the original distances of the clustering plot)

	Manxcat SMACOF		WDA-SMACOF
	revised 599nts	999nts	revised 599nts	999nts
SWG	19.37	19.89	16.01	12.74
MSA	16.62	16.36	15.20	13.65

1) revised 599nts spherical tree

MSA Result

SWG Result

2) 999nts spherical tree

MSA Result

SWG Result

Pairwise Distances from MSA Vs Pairwise Local Alignment Distances for Revised 599Nts

Following heatmap present the correlation between distances computed from multiple sequence alignment (MSA) versus pairwise local alignment for revised 599Nts dataset (MSA is available here and sequence file is here).

Details on MSA based distance computation is at http://salsafungiphy.blogspot.com/2013/06/pairwise-distance-calculation.html

Details on pairwise local alignment based distance computation is at http://salsafungiphy.blogspot.com/2012/10/pairwise-distances-from-multiple.html

Summary of Multi-Dimensional Scaling Runs