Question: Best Way To Check Topology Support For A Phylogenetic Tree
1
gravatar for Pappu
7.2 years ago by
Pappu1.9k
Pappu1.9k wrote:

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.

phylogenetics • 1.9k views
ADD COMMENTlink modified 6.9 years ago by Biostar ♦♦ 20 • written 7.2 years ago by Pappu1.9k
4
gravatar for Zev.Kronenberg
7.2 years ago by
United States
Zev.Kronenberg11k wrote:

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.

ADD COMMENTlink modified 7.2 years ago • written 7.2 years ago by Zev.Kronenberg11k

+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.)

ADD REPLYlink written 7.2 years ago by Josh Herr5.7k

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

ADD REPLYlink written 7.2 years ago by Zev.Kronenberg11k

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.

ADD REPLYlink written 7.2 years ago by Josh Herr5.7k
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