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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl HYPHY Package >> HyPhy feedback >> Ancestral state reconstructions in HyPhy http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1311715752 Message started by Dan Fulop on Jul 26^th, 2011 at 2:29pm

Title: Ancestral state reconstructions in HyPhy
Post by Dan Fulop on Jul 26^th, 2011 at 2:29pm

Hi,

I'm wondering if the ancestral state reconstruction methods available in Datamonkey under the ASR module are also implemented/available in HyPhy.

Obviously, they're implemented in HyPhy as Datamonkey uses HyPhy on the backend, etc. But, I can't find any such analyses under the "Standard Anlyses" menu in the HyPhy GUI, so I can't see what options I need to code a script, etc. ...I haven't yet looked in the command line...

Thanks,
Dan.

Title: Re: Ancestral state reconstructions in HyPhy
Post by Sergei on Jul 26^th, 2011 at 2:36pm

Hi Dan,

They are accessible in a somewhat limited fashion. Take a look at post_ancestors.bf in TemplateBatchFiles (simple case).

Sergei

Title: Re: Ancestral state reconstructions in HyPhy
Post by Dan Fulop on Jul 26^th, 2011 at 2:48pm

Hi Sergei,

Thanks for the prompt reply.

A simple implementation is actually better than what we're using right now. Plus, I don't think we could apply the more complex methods to ~14K genes in a reasonable amount of time.

Cheers,
Dan.

Title: Re: Ancestral state reconstructions in HyPhy
Post by Dan Fulop on Jul 26^th, 2011 at 3:28pm

I can feed it either a nucleotide or a codon model fit, right?

We're looking at losses and gains of stop codons, so using a codon model for the reconstructions would be more appropriate. Would you agree?