Dear all,

I am trying to see if the phylogenetic trees I constructed support a topological hypothesis that a certain group of organisms is monophyletic. I can of course eye-ball the tree to see if it's correct, but the question is that, I have thousands of trees... Actually I am trying to compute the posterior probability of a topological hypothesis from a MrBayes tree sample file (.t). Therefore, I am seeking an automatical way to scan all these 1000 trees and count how many of them match a topological constraint I provide. The principle is simple. I'm just wondering if there is already a tool out there. Anyone has any thoughts? Thanks!

Best wishes

look into hypothesis testing. The KH test is pretty good and is implemeted in many tools. E.g. check this presentation by Mark Holder http://phylo.bio.ku.edu/woodshole/HolderTestingLectureWoodsHole2012.pdf