What Is The Best R Package For Phylogenetic Tree Partionning ?

Question

[Radhouane Aniba]

Hi everyone,

I am working on a project where I have a phylogenetic tree and an enrichment score for Transcription factor corresponding to each leaf (specie);

what I want to do is to know in which internal branch there is a significant shift in these enrichment score which will point to something that happened during evolution in that branch;

I would like to know which is the best R package that could be used to do such analysis and to assign statistical measure to that shift, I am thinking about a package that could run permutations and partitioning cutting the tree for a certain number of tests and measuring the difference in enrichment scores using a wilcoxon test for example, it is just a way of doing this;

Any help that point for the right or most appropriate R package is appreciated

Cheers

Radhouane

Answer 1

[DG]

Probably Ape or R-Brownie would be your best bet. Ape is a pretty extensive library of phylogenetic methods for R and RBrownie includes things like ancestral state reconstruction. Between the two of them you should be able to devise an appropriate test/workflow.