The ortholog groups of 5 species proteins look like:
Group1: sp1 sp2 sp3 sp4 sp5
Group2: sp1 sp2_seq1 sp2_seq2 sp3 sp4_seq1 sp4_seq2 sp5
(sp is for species here)
As here one can see the Group1 have 1 sequence for all 5 species but Group2 have two sequence for species 2 and species 5.
Do I need to reduce the Group2 cluster before analysis of selection pressure. I assume using co-orholog (like sp2_seq1 sp2_seq2 and sp4_seq1 sp4_seq2 ) might result biasedness towards these species in the analysis.