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purifying selection branch-site REL (Read 1684 times)
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Curious HyPhy user

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purifying selection branch-site REL
Jul 30th, 2013 at 12:12pm

Sorry if this is a silly question but how do I identify purifying selection of branches using branch-site REL? I am looking over the associated publication, Kosakovsky Pond et al., 2011, and I'm assuming that I can extract the information I need from table 2 but I'm not sure.

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Datamonkeys are forever...

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Re: purifying selection branch-site REL
Reply #1 - Aug 7th, 2013 at 1:36pm
Hi Andrew,

Branch-site REL does not directly test for purifying selection, so you can't extract the information about it from the results table. You can get an indication of what the selection profile looks like, but there is no formal test. You could readily modify the test to ask questions about dN/dS < 1 (i.e. is there a proportion of sites along a branch where dN/dS), but I think for the vast majority of branches in the vast majority of data sets the answer is yes by default, i.e. one will have to work hard to find branches where no sites evolve with dN/dS < 1.

Can I ask why you wish to run this test?

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