HyPhy message board - Print Page

HyPhy message board
http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl Theoretical questions >> Sequence Analysis >> different rate matrix for every codon http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1378197893 Message started by YuanlingRui on Sep 3^rd, 2013 at 1:44am

Title: different rate matrix for every codon
Post by YuanlingRui on 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

Title: Re: different rate matrix for every codon
Post by Sergei on 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

Title: Re: different rate matrix for every codon
Post by YuanlingRui on 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

Title: Re: different rate matrix for every codon
Post by YuanlingRui on 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