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Sliding windows purifying selection (Read 1835 times)
Ed
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Curious HyPhy user

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Sliding windows purifying selection
May 3rd, 2012 at 7:32pm
 
Hello guys,

I have a flu dataset for which we would like to look at evolutionarily conserved sites, similar to the analysis done in:

Ngandu, N. K., Scheffler, K., Moore, P., Woodman, Z., Martin, D., & Seoighe, C. (2008). Extensive purifying selection acting on synonymous sites in HIV-1 Group M sequences. Virology Journal, 5, 160.

with HIV data. Is there any way to perform such analysis with the current HyPhy version? if yes, what would be the batch file? If not, is there any way to get the batch file used?

Thanks in advance

Ed
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Sergei
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Datamonkeys are forever...

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Re: Sliding windows purifying selection
Reply #1 - May 5th, 2012 at 7:23pm
 
Hi Ed,

There is a sliding window analysis in HyPhy -- Standard Analyses:Miscellaneous:SlidingWindowAnalysis.bf
I would give that a try with a locally parameterized codon model.

Sergei
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Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego
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Ed
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Re: Sliding windows purifying selection
Reply #2 - May 6th, 2012 at 11:36pm
 
Thanks Sergei!

Ed
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