ensembl tree
rresendepinto opened this issue · 1 comments
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
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