Robinson-Foulds Distances

Here we present the Robinson-Foulds metric computed for trees with 2133 and 200 Fungi taxa. Details on these datasets are presented at http://salsafungiphy.blogspot.com/2012/11/tree-distance-heatmaps.html

Metric for Fungi 2133

We have following five trees generated with this dataset.

• Tree A
  • Pairwise sequence alignment with Smith-Waterman algorithm using EDNAFULL scoring matrix and gap penalties –16 and –4 for gap open and gap extension respectively.
  • Distance measure between sequences is percent identity
  • Tree created with Ninja
• Tree B
  • Multiple sequence alignment with MUSCLE
  • Tree created with RAxML
• Tree C
  • Distance between sequences are taken as the 3D distance resulted from DA-SMACOF dimensional scaling of the Smith-Waterman percent identity distances (used in Tree A).
  • Tree created with Ninja
• Tree D
  • Distance between sequences are taken as the 10D distance resulted from Manxcat (dimensional scaling  program) running in SMACOF mode for the Smith-Waterman percent identity distances (used in Tree A).
  • Tree created with Ninja
• Tree E
  • Distance between sequences are taken as the 10D distance resulted from DA-SMACOF dimensional scaling of the Smith-Waterman percent identity distances (used in Tree A).
  • Tree created with Ninja

Robinson-Foulds metric for trees

• The metric is computed with PHYLIP package found at http://evolution.genetics.washington.edu/phylip.html

	Tree A	Tree  B	Tree C	Tree D	Tree E
Tree A	0	3484	3966	3726	3740
Tree B	3484	0	3956	3796	3806
Tree C	3966	3956	0	3438	3392
Tree D	3726	3796	3438	0	1282
Tree E	3740	3806	3392	1282	0