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Filtering gene trees generated by RAXML

Hey guys,

What is the best way to checking if a set of gene/homolog trees, (about a 1000 tree files), has a certain amount of taxa within them? Baring in mind, you want the trees to also include an outgroup taxon as well.

I was thinking about using python along with a dictionary to check for this, but I don't know of any way to make tree files readable objects in python.

Instead, of python are there any R packages that could help me do this.

Or am I approaching this wrong? Any thoughts?

Thanks in advance!

python r raxml
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updated by h.mon h.mon • written by apulunuj • apulunuj

1 answer

I don't understand, did you run the analysis that generated the trees? If yes, then you should know which taxa are included.

Check ETE for a tree manipulation toolkit, it probably can parse the trees for you.

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written by h.mon h.mon

Yes, I generated the trees. But not all the trees are inclusive of the taxa I'm interested in. And there are too many trees to look through by hand.

Will the ETE toolkit allow me as you say parse the non-inclusive trees?

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written by apulunuj • apulunuj

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