I've been using OMA standalone to identify orthologs and their evolution in my data set. Couple of species in my data set include splice variants, so as described in the manual, I included
.splice files. Analyses went smoothly,
used_splicing_variants.txt appeared in the output folder, and it looks fine.
But, when I analyzed
HierarchicalGroups.orthoxml (or other .orthoxml files) I realized that each splice variant is encoded as a separate gene.
.orthoxml file was used (with pyHam) to infer number of gene families with duplications, number of gained/lost genes, but now I'm not sure how to interpret these results. PyHam seems to interpret each splice variant as a separate gene and number of "gene gains" sum up to number of transcripts. Is there a way to use only one splice variant per gene in the PyHam analyses with OMA output?
Thanks in advance!