Using ete3 without knowing tree topology
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!
1 answer
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
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Michael Dondrup
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If you have the alignment you can make the tree with many different tools:
RAxMLis good but not overly user friendly,fasttreeis simple and quick.You can then use
ete3to compare the trees and do whatever else you want to do.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.