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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl HYPHY Package >> HyPhy bugs >> specifying the matrix http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1162918934 Message started by kateveronica on Nov 7^th, 2006 at 9:02am

Title: specifying the matrix
Post by kateveronica on Nov 7^th, 2006 at 9:02am

Hey Guys,
I am a newby to hyphy and bioinformatics as a whole. I was following the tutorial. After partiitioning the data for p_51.nex sample data, I chose the p_51 tree and tried to specify the substitution/matrix model to be HKY85 inorder to be able to get a likelihood function. My only choice when I went to the dropdown menu was "none". the Likelihood function cannot be carried out without out a tree and a "model". What am I missing here? Thanks,
Kate

Title: Re: specifying the matrix
Post by Sergei on Nov 7^th, 2006 at 9:20am

Dear Kate,

My first guess would be that HyPhy is not reading model definitions from its install directory. You can check this by opening the Object Inspector, and looking under the Models tab to see if there are some models (including HKY85) listed there.

What OS are you running HyPhy under?

Cheers,
Sergei

Title: Re: specifying the matrix
Post by kateveronica on Nov 7^th, 2006 at 4:03pm

Sorry, I meant to include what OS I am using in the original question. Mine is Mac OS X 10.4.8. Does that mean something regarding hyphy? I will try your suggestion and bug you again if I still have problems. Thanks alot for your help,
kate

Title: Re: specifying the matrix
Post by Sergei on Nov 7^th, 2006 at 4:22pm

Dear Kate,

The OS determines (to an extent) how HyPhy decides where to look for its components.

Cheers,
Sergei