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Will hyphy easily do this codeml analysis? (Read 1845 times)
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Will hyphy easily do this codeml analysis?
Jan 2nd, 2013 at 4:34pm

I am thinking of pillaging some of Kimura's old work, to put more population genetic parameters into substitution rate matrices, and I am preliminarily wanting to reproduce the last couple rows of Table (1) of
"Mutation-Selection Models of Codon Substitution and Their Use to Estimate Selective Strengths on Codon Usage"
Ziheng Yang and Rasmus Nielsen (2008)
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I do not want to make my modifications directly to Ziheng Yang's code, because that source code is too hard for me to understand.  On the other hand I've written some one-off python scripts which are able to do this maximum likelihood estimation well enough to reproduce the last couple of rows of that table.

Maybe I would save time by using HyPhy instead of custom python scripts for the rest of the project?  I don't know HyPhy well enough to decide.  Is every analysis that PAML does also fair game for HyPhy?  Or are there things that PAML does which are outside the intended scope of HyPhy?
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Datamonkeys are forever...

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Re: Will hyphy easily do this codeml analysis?
Reply #1 - Jan 4th, 2013 at 10:02am
Hi Alex,

Generally speaking PAML-type analyses are relatively easy to implement in HyPhy, especially if all you are doing is defining a rate matrix. HyPhy was almost tailor-made for that. Let me know if you need help along the way.

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