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GA branch analysis (Read 2095 times)

DCM YaBB Newbies Offline Feed your monkey! Posts: 1	GA branch analysis May 13^th, 2011 at 3:46pm Greetings, I have a set of 50 HIV sequences on which I would like to perform a GA branch analysis but I know that the current maximum number of sequences you can upload is 30. Would it be possible to increase this upper limit? If not, do you have suggestions on how to proceed so that the analysis is not too biased? Thank you very much, DCM.
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Sergei

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Re: GA branch analysis
Reply #1 - May 13^th, 2011 at 3:52pm

Hi DCM,

GA Branch is soon going to be replaced by a new method (Branch Site REL), described in an upcoming MBE manuscript (preprint attached); the main advantage of the new model is that it can model site-to-site rate heterogeneity as well. It'll be up on Datamonkey soon.

A brief description of how to run this method on your own machine (if you have HyPhy installed) can be found here

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

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