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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl Methodology Questions >> How to >> Estimation of gamma shape and pinv among codons http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1273831031 Message started by Miguel on May 14^th, 2010 at 2:57am

Title: Estimation of gamma shape and pinv among codons
Post by Miguel on May 14^th, 2010 at 2:57am

Hi all,

I would like to ask you for a possible option in Hyphy.
For an alignment of coding sequences, I am interested in to estimate the gamma shape and the proportion of invariable sites of the substitution rate among codons (not among nucleotides). Note that modelTest (D. Posada) allows the estimation of G + I among nucleotides, but here we are interested in the estimation among codons and we do not know if Hyphy could do this.

So, is it possible with Hyphy? if yes, what is the batch file or olption in the menu for such estimation?

Thanks! ::)

Cheers,
Miguel

Title: Re: Estimation of gamma shape and pinv among codons
Post by Sergei on May 14^th, 2010 at 4:39am

Hi Miguel,

AnalyzeCodonModel.bf will do it. Select the model you want, then global w/variation for model options, then Gamma+Inv etc. Note that this will apply the same distribution to both syn and non-syn rates, i.e. is directly analogous to the nucleotide case.

Sergei

Title: Re: Estimation of gamma shape and pinv among codons
Post by Miguel on May 14^th, 2010 at 5:14am

Hi Sergei,

That's Great!. But, I do not find that batch file (AnalyzeCodonModel.bf), is it in the Hyphy package? could you send it me?. Thanks. :)

Best,
Miguel

Title: Re: Estimation of gamma shape and pinv among codons
Post by Sergei on May 14^th, 2010 at 5:57am

Hi Miguel,

Sorry, I meant AnalyzeCodonData.bf (it's in standard analyses under simple analyses).

S.