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Methodology Questions >> How to >> REV with different rate matrix for one branch http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1268189297 Message started by Alan dQ on Mar 9th, 2010 at 6:48pm |
Title: REV with different rate matrix for one branch Post by Alan dQ on Mar 9th, 2010 at 6:48pm
Hello Sergei,
I'm analyzing a data set consisting of a bunch of mitochondrial sequences and a single paralogous nuclear-mitochondrial pseudogene. I'd like to estimate branch lengths using a REV model in which all the mt branches have a common rate matrix and the pseudogene branch has a different matrix (with the rate parameter values all estimated from the data). Is it possible to do this in HYPHY and, if so, how? The (or at least one) problem is that I don't know how to specify the REV global model in the batch file. I've gotten it to estimate shared rate parameters but the tree produced was ultrametric. |
Title: Re: REV with different rate matrix for one branch Post by Alan dQ on Mar 10th, 2010 at 12:26pm
Sergei, Thanks very much for the quick reply. That did exactly what I wanted it to do.
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