Question: Using ete3 without knowing tree topology
0
gravatar for jyu429
2.7 years ago by
jyu429120
United States
jyu429120 wrote:

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!

phylogenetic tree ete3 • 791 views
ADD COMMENTlink modified 2.6 years ago by Biostar ♦♦ 20 • written 2.7 years ago by jyu429120

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.

ADD REPLYlink written 2.7 years ago by Joe14k
1

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.

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by Michael Dondrup46k
0
gravatar for Michael Dondrup
2.7 years ago by
Bergen, Norway
Michael Dondrup46k wrote:

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

ADD COMMENTlink written 2.7 years ago by Michael Dondrup46k
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