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gamma distribution in HyPhy (Read 2618 times)

laura

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gamma distribution in HyPhy
Oct 30^th, 2009 at 8:09am

I am a new user to HyPhy and a beginner in bioinformatics. I am using HIV-1 gene sequences to find positive selection in primates lentivirus lineages (therefore, I am looking for dN/dS ratios). I am currently working through the example, applying a codon model to integrase_BDA.nex, found in the article ‘HyPhy: Hypothesis Testing Using Phylogenies’ pg 21. I was wondering if it was possible to include a gamma distribution variable during the procedure?

Many thanks for your time, Laura

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Sergei

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Re: gamma distribution in HyPhy
Reply #1 - Oct 30^th, 2009 at 9:09am

Dear Laura,

You can indeed include the gamma (and a wealth of other distributions).

The easiest place to start is Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to

Login - an online server to screen sequences for positive selection. You will find a lot of information and detailed worked-through examples focusing on positive selection detection in our book chapter on the topic, which can be downloaded from Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to

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

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leh123 YaBB Newbies Offline Feed your monkey! Posts: 1	Re: gamma distribution in HyPhy Reply #2 - Jan 31^st, 2010 at 2:23am Thanks for your reply - I have read the document you referred me to and it appears that the gamma distribution can be applied only on a site by site basis as opposed to on a branch by branch basis - is this correct?
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