Using ete3 without knowing tree topology

Question

[jyu429]

Hi,

I would like to start using ETE Toolkit (http://etetoolkit.org/) for creating a phylogenetic tree from DNA sequences from severla human individuals. I already have the alignment, but it seems like you have to specify and know the topology of the tree beforehand. Is there a way to infer the topology using ETE? Thank you!

[Joe]

If you have the alignment you can make the tree with many different tools: RAxML is good but not overly user friendly, fasttree is simple and quick.

You can then use ete3 to compare the trees and do whatever else you want to do.

[Michael]

Most used is probably MrBayes. State of the art seems to be to make a set of Bayesian trees, Maximum likelihood trees (RAxML or PhyML), then compute a consensus tree.

Answer 1

[Michael]

You need to infer a phylogeny using a software made for that purpose and give that as input. http://evolution.genetics.washington.edu/phylip/software.html