Dear HyPhy Team,

I am a Phd student and have the following query re selection analysis/HyPhy. Can you please help me with the following.

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 (or in simple words just have 1-1 relations). 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 or the orthomcl cluster directly can go as input to HyPhy?

Many thanks and kindest regards,
Ritu

Hi Ritu,

I am not familiar with orthomcl, so I can't really help you there. You can run HyPhy/PAML etc on any alignment you'd like, but the interpretation will differ. One issue with gene families is gene conversion, which can bias detection analyses (see Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login and Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login). Datamonkey/HyPhy can handle this. Another issue is that different gene family members can be under different selective pressures, so you need a model that can handle branch-site variation (like MEME or BranchSite REL in HyPhy). Finally, you can have pseudogeneziation, where codon models no longer apply. You need to decide how to interpret the results based on your particular gene family.

Take a look at how other people have analyzed gene families with datamonkey for some further pointers: Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login

Sergei