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Site heterogeneity in equilibrium frequencies (Read 2369 times)

Miguel Lacerda

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Site heterogeneity in equilibrium frequencies
Jul 25^th, 2008 at 7:23am

Hi,

Quick question: Is it possible to model site-heterogeneity in equilibrium frequencies in HyPhy and if so, what is the easiest way to do this? I have tried using the "category" statement to define a variable (drawn from a discretized beta distribution) and expressing my codon frequencies as a function of this variable, but this does not seem to work. Can the "category" statement only be used in conjunction with the rate matrix - or is it also applicable to the vector of equilibrium frequencies?

Thanks,
Miguel

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Sergei

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Re: Site heterogeneity in equilibrium frequencies
Reply #1 - Jul 25^th, 2008 at 9:21am

Dear Miguel,

RV in EF should work, but now that you mention it, I think the implementation may not support it properly. Can you attach the batch files you tried? I'll run them through and see if the code is behaving properly.

There is an uglier way to implement arbitrary rate variation models; if the category approach does not work, I'll show you how.

Cheers,
Sergei

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

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Miguel Lacerda YaBB Newbies Offline Feed your monkey! Posts: 36 Natl Univ of Ireland, Galway Gender:	Re: Site heterogeneity in equilibrium frequencies Reply #2 - Jul 28^th, 2008 at 8:48am Hi Sergei Thanks for your quick reply! I have managed to figure out my (stupid) mistake - I simply forgot to use double underscores in my specification of the EFs and it only caused an error message when I allowed for RV in the EFs. Everything seems to be working now! Thanks again, Miguel
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