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test for synonymous substitution variation (Read 2244 times)

Donna Toleno

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test for synonymous substitution variation
Oct 10^th, 2006 at 1:27pm

I would like to compare the nested models referred to as Dual and Non-synonymous in Pond and Muse, 2005 "Site-to-site variation of synonymous substitution rates." I would like to test for synonymous rate variation among partitions of the data (10 different genes). I have a total of over 2000 codons from 19 species.

A possibly unrelated question... I am not sure I understand the difference between MG94W9 and MG94X2. Are these nested models?

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Sergei

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Datamonkeys are forever...

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Re: test for synonymous substitution variation
Reply #1 - Oct 10^th, 2006 at 2:04pm

Dear Donna,

The Non-synonymous and Dual models are implemented in the Standard Analysis located under "Codon Selection Analyses:dNdSRateAnalysis.bf". You should select both Non-synonymous and Dual in the models of rate variation dialog, when it appears. This will fit both models and report a LR test for significance.

Cheers,
Sergei

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

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