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DessimozLab / pyham

MIT License
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ensembl tree #24

Open rresendepinto opened 1 year ago

rresendepinto commented 1 year ago

Hi!

I am trying to use pyham with orthoxml files from ensembl but I am struggling to understand which species tree I can get from ensembl to use in pyham.

For ensembl data, it needs to be a newick tree, right? And can I get an overall tree that will work for all orthoxml files or do I need a specific one for each file/HOG?

Thank you!

Rui

alpae commented 1 year ago

Hi @rresendepinto ,

the species tree should be in agreement with the orthologGroup nesting and the species that are inside it. Generally speaking, a single species tree should be ok to work with all the orthoxml files from a single source. usually the species tree is fixed for a resources and all the orthology/paralogy delineation is based on the same tree.

I hope this answers your question.

Best wishes Adrian