I have the following query re the selection analysis using codeml/HyPhy.
The objective of my work is to test whether the set of genes are under selection pressure or not. I have used orthomcl to extract orthology clusters for my dataset.
Most of the literature I have seen study selection pressure on single-copy orthologs ( gene that have 1-1 orthologs in the species of interest). What should I do in case of multigene families? Does HyPhy/Codeml works well in case of multi gene families? Do I have to extract 1-1 relations from these families and then input to codeml/hyphy or the orthomcl cluster directly can go as input to HyPhy?
Many thanks, Rtu