Tree Distance Heatmaps

This is an attempt to find a “goodness” measure for phylogenetic trees generated by programs such as Ninja (http://nimbletwist.com/software/ninja/index.html) or RAxML (http://www.phylo.org/news/RAxML). 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.

• Edge Sum
  • 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.
• Edge Count
  • Given two sequence A and B, we find the shortest path from A to B and count the number of edges in it.

We have performed this analysis for two datasets.

• Fungi 200 https://www.sugarsync.com/pf/D6858752_2739277_6854163
  • 126 sequences (in reverse complemented form) represent the centers for clusters in http://salsahpc.indiana.edu/millionseq/haixu/fungi_index.html (note. restricted access)
  • 74 sequences from GenBank
• Fungi 2133 https://www.sugarsync.com/pf/D6858752_0743775_6281705
  • 126 sequences (in reverse complemented form) represent the centers for clusters in http://salsahpc.indiana.edu/millionseq/haixu/fungi_index.html (note. restricted access)
  • 74 sequences from GenBank
  • 988 sequences from Kruger et. al. dataset
  • 945 sequences from Wittiya’s dataset

Heatmaps for Fungi 200

3D DA-SMACOF of SWG PID Vs SWG PID
Edge Sum Ninja from SWG PID Vs 3D DA-SMACOF of SWG PID	Edge Sum Ninja from SWG PID Vs SWG PID

Heatmaps of Fungi 2133

3D DA-SMACOF of SWG PID Vs SWG PID
Edge Sum Ninja from 3D DA-SMACOF of SWG PID Vs 3D DA-SMACOF of SWG PID	Edge Sum Ninja from 3D DA-SMACOF of SWG PID Vs SWG PID
Edge Sum RAxML(20 iterations) from ClustlO MSA Vs SWG PID	Edge Sum RAxML (20 iterations) from ClustlO MSA (distances from 0 to 0.15) Vs SWG PID
Edge SumRAxML(20 iterations) from ClustlO MSA Vs Strict PIDNG	Edge Sum RAxML (20 iterations) from ClustlO MSA (distances from 0 to 0.15) Vs Strict PIDNG