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How to run M1a/M2a test with syn rate variation (Read 3041 times)

CGS

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How to run M1a/M2a test with syn rate variation
Feb 29^th, 2008 at 12:07pm

Dear all,
I have run the Dual/Nonsynonymous test suggested in Kosakovsky Pond et al (2005, MBE) to check for syn rate heterogeneity in my data and I've got significant LRT. Now I would like to run a test analogous to the M1a/M2a model comparison in PAML4, but allowing synonymous rate variation. Any suggestions?
Thanks!

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Sergei

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Re: How to run M1a/M2a test with syn rate variatio
Reply #1 - Feb 29^th, 2008 at 12:14pm

Dear CGS,

Try the PARRIS (Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to

Login) test designed by Konrad Scheffler and colleagues. You can run it in HyPhy (under Selection/Recombination) and also on datamonkey.org

You can also take a look at Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to

Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego

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CGS

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Re: How to run M1a/M2a test with syn rate variatio
Reply #2 - Feb 29^th, 2008 at 12:29pm

Hi Sergei.
I've run the PARRIS test but I am not sure whether it uses a model analogous to the M1a/M2a or the former M1/M2 implemented in older versions of paml. Does parris allow the omega parameter of the negative selection class to be estimated or fix it at zero?
Here are my PARRIS settings:
inputRedirect["05"]="Codon Model";
inputRedirect["06"]="MG";
inputRedirect["07"]="HKY85";
inputRedirect["08"]="Single";
inputRedirect["10"]="Dual";
inputRedirect["11"]="Independent";
inputRedirect["12"]="Nucleotide (syn3)";
inputRedirect["13"]="PARRIS";
inputRedirect["14"]="Default";
Cheers.

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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: How to run M1a/M2a test with syn rate variatio Reply #3 - Feb 29^th, 2008 at 10:11pm Dear CGS, If memory serves, PARRIS should be analogous to M1a/M2a in that the omega < 1 class has its omega estimated and not fixed at 0. Cheers, Sergei
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CGS YaBB Newbies Offline Feed your monkey! Posts: 8	Re: How to run M1a/M2a test with syn rate variatio Reply #4 - Mar 1^st, 2008 at 7:45am That's right. I've just checked the paper of Scheffler and colleagues. The omega < 1 parameter is inferred. Thanks Sergei!
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