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combined single and dinucleotide subsitution model (Read 1125 times)

eliot YaBB Newbies Offline I love YaBB 1G - SP1! Posts: 9	combined single and dinucleotide subsitution model May 14^th, 2007 at 7:49am I'm interested in using a substitution model which contains rates for single nucleotide changes and also some for dinucleotides (e.g. CG to CA/TG). This would be something like what was done by Arndt, Petrov, and Hwa 2003 (MBE). Is it possible to do this in HYPHY?
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Sergei

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Re: combined single and dinucleotide subsitution
Reply #1 - May 14^th, 2007 at 10:14am

Dear eliot,

It is indeed possible. You can either define an arbitrary 16x16 substitution model; alternatively you can partition the data into those sites which are evolving under the paired model and those which are evolving under the nucleotide model and analyze them as mixed data, where each partition is assigned its own appropriate model.

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Sergei

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

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