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different rate matrix for every codon (Read 4515 times)
YuanlingRui
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different rate matrix for every codon
Sep 3rd, 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 5th, 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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YuanlingRui
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Re: different rate matrix for every codon
Reply #2 - Sep 9th, 2013 at 1:39am
 
Hi Sergei,
    Thank you for answer, when I write out the prototype code, I will ask for you help again.

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Yuanling
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YuanlingRui
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Re: different rate matrix for every codon
Reply #3 - Oct 26th, 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!

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Yuanling
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