Heatmaps of 10D vs 3D vs SWG

Here we list heatmaps of distances resulted from dimensional scaling versus original Smith-Waterman for two datasets. The description of distances is as follows.

• SWG PID
• 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 http://salsafungiphy.blogspot.com/2012/10/heatmaps-of-different-distances.html
• 10D
• The 10 dimensional Euclidean distance based on DA-SMACOF mapping of SWG PID
• 3D
• The 3 dimensional Euclidean distance based on DA-SMACOF mapping of SWG PID

The two datasets are described at http://salsafungiphy.blogspot.com/2012/11/tree-distance-heatmaps.html

 

Heatmaps for Fungi 200

 

3D DA-SMACOF of SWG PID Vs SWG PID	10D DA-SMACOF of SWG PID Vs SWG PID
10D DA-SMACOF of SWG PID Vs 3D DA-SMACOF of SWG PID

Heatmaps for Fungi 2133

3D DA-SMACOF of SWG PID Vs SWG PID	10D DA-SMACOF of SWG PID Vs SWG PID
10D DA-SMACOF of SWG PID Vs 3D DA-SMACOF of SWG PID