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.
Hi Ashmit,
I would first try to make a phylogeny, or at least "fit" the genes in a species phylogeny. The more you know about the origin and evolutionary relationships between your homologs, the better you will be able to answer this question, I guess.
e.g. are seq1 and seq2 in sp1 and sp4 the same duplication? Are the single copy orthologs in group 2 all more related to either of both paralogs in sp1 and sp4? In that case other paralogs may have gone lost in the other linaeges.
If you find that in group 2, the pairs of orthologs (with respect to group 1) are real paralogs of each other, I guess you can just treat them as separate orthologs, since selection pressure need not be the same for both copies (typically it is not).
So in that case you would compare Sp2 to both sp2_seq1 and sp2_seq2.
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