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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl HYPHY Package >> HyPhy feedback >> non-reversible models http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1170445085 Message started by konrad on Feb 2^nd, 2007 at 11:38am

Title: non-reversible models
Post by konrad on Feb 2^nd, 2007 at 11:38am

Hi Sergei,

Does HyPhy support non-reversible models? I'm asking because some mathematical shortcuts assume reversibility, so if these are used in the implementation specifying a non-symmetric rate matrix will give incorrect results.

cheers,
Konrad

Title: Re: non-reversible models
Post by Sergei on Feb 2^nd, 2007 at 2:59pm

Dear Konrad,

HyPhy core does not make any assumptions which rely on time reversibility, hence you can specify non-reversible models in the batch language and the calculations will be correct. The only assumption (which you can override with the ACCEPT_ROOTED_TREES = 1 flag in the code) is that trees can be 'unrooted' and 'rerooted' at will - rerooting a tree will, in general, change the results under a non-reversible model.

Cheers,
Sergei