Best Way To Check Topology Support For A Phylogenetic Tree

Question

[Pappu]

I made phylogenetic tree using FastTree of an alignment ~2000 protein sequences. I am willing to know how the topology support for the branches can be checked since bootstrap is not feasible here. I am also wondering how to simplify such huge tree and name the branches. Thank you.

Answer 1

[Zev.Kronenberg]

Bootstrap is alway feasible. I bootstrapped an entire genome.

An idea:

Build a consensus tree from all the genes.

Sub sample some trees and ask how many times each bifurcation in the global/consensus tree is supported by the subset of trees.

This is a bootstrapping approach.

[Josh Herr]

+1, great strategy for topology support. Did you write a script to do this or is there a quick option on one of the programs of choice that I don't know about? (Forgive my ignorance, but I haven't read a lot of the manuals in detail to know right away.)

[Zev.Kronenberg]

I think you could do it using APE in [R]. APE has tons of tree methodology.

[Josh Herr]

Thanks! I'm going to check APE out. That's one of those packages that I installed but haven't had time to actually look at yet.