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different rate matrix for every codon (Read 3712 times)

YuanlingRui

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different rate matrix for every codon
Sep 3^rd, 2013 at 1:44am

Dear Hyphy users,
I am doing some work about coding sequences evolution that giving different rate matrix (Q matrix) for every codon. I want to know, 1) whether do I have to use the function LikelihoodFunction id = (datafilterid_0,tree_0,...,<datafilterid_n>,<tree_n>,), in which the n is codon number; 2) if I have to use the function, how about the time-consuming.
Thank you very much!

Regards!
Yuanling Xia

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Sergei

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Re: different rate matrix for every codon
Reply #1 - Sep 5^th, 2013 at 1:59pm

Hi Yuanling,

In the most general case, you do need to use the form you describe. You probably also want to constrain branch lengths between trees on each codon, otherwise you'll have a separate set of branch lengths (e.g. the t parameter) for every codon. Do you have prototype code? I can look at it and help you ensure that everything works smoothly and correctly.

Sergei

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University of California San Diego

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YuanlingRui YaBB Newbies Offline Curious HyPhy user Posts: 3	Re: different rate matrix for every codon Reply #2 - Sep 9^th, 2013 at 1:39am Hi Sergei, Thank you for answer, when I write out the prototype code, I will ask for you help again. Regards Yuanling
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YuanlingRui YaBB Newbies Offline Curious HyPhy user Posts: 3	Re: different rate matrix for every codon Reply #3 - Oct 26^th, 2013 at 7:44pm Hi Sergei, I have send the prototype code to you. The time-consuming will increase greatly when I give many partitions using function LikelihoodFunction. Thank you very much! Regards Yuanling
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