I have done positive selection analysis using one-to-one copy ortholog groups via codeml tool. But I have seen some papers in which multiple copy gene ortholog families were also used to test positive selection. When I tried to do same analysis (multiple copy approach), ETE tool used only one sequence (one gene) from each species although each species has multiple copies in the same ortholog family.
Is there any way to deal with gene duplication event because ETE uses only the first sequence of each species?
Codeml in PAML says Seq occurs more than once in the alignment.
Any of you has done this kind of analysis (using multiple copy orthologs) before?