Hi there,

I am a new user to Datamonkey (and more generally to molecular evloution) and like its flexible and user friendly intereface.

I am testing a hypothesis that selective constraints were altered within a specific lineage of a set of vertebrate orthologues. I have used GA-branch to establish that indeed, functional constraints were relaxed at the base of the lineage in question (marked and significant increase in dN/dS) and this seems to be ongoing in later branches.

I have used SLAC, FEL, REL approaches to identify selective pressures at different sites in the alignment as a whole, which identified a mass of sites under strong purifying selection. However, I really wish to know if I can identify constaints at sites in specific parts, or along particular branches of the phylogeny?, Is there any way that datamonkey can do this, or would I require the use of HyPhy software? I am pretty sure such analyses can be explored in PAML...

Alternatively, considering that I gained support with GA-branch for my original hypothesis, would a reasonable alternative be to use SLAC, REL etc with a codon alignment of orthologues solely from the lineage with suspected altered constraints and then just visually examine individual sites identified in the context of their phylogentic relationships?

I hope my naivity with molecular evolution is not too evident and thankyou very much for your help with this! 

Regards

Dan

Dear Sergei,

Hi, and thanks for your quick response. I have the book chapter from the 'phylogentic handbook' 2009 edition and have found it most helpful in getting to grips with HyPhy.

I have a quick question though 

I have compared selective constraints between two clades in my phylogeny and their seperating branch using the selection LRT function, which gave me an interesting result. I now wish to examine site to site variation in rates specifically in the seperating branch and also in branches within one of the clades relative to background branches.

I would like to use a two rate FEL to explore this , but am unsure about the difference in 'subtree only' and 'custom subset' options. In the example provided for the data set (mammalsbirds.nex, which I cant find in any folders? It would be helpful to get this if possible?) it is not clear which option leads to the 'branch-site' type analysis to examine the specific node (seperating branch) in question.

Thus, in summary, I want to examine those specific sites with evidence of significant deviation from neutral selection in the seperating branch of interest- it would be great if you could just confirm to me which option will allow me to do this.

Thanks again and all the best

Dan