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Methodology Questions >> How to >> "Free-ratios"-like analysis in PAML http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1122383405 Message started by avilella on Jul 26th, 2005 at 6:10am |
Title: "Free-ratios"-like analysis in PAML Post by avilella on Jul 26th, 2005 at 6:10am
Dears,
I would like to know if it is possible to analyse a 4-species alignment in a similar fashion as the "Free-ratios" model in PAML. Specifically, I would like to specify that each branch has it's own omega ratio. For what I see, I should use BranchClassDNDS.bf (or maybe SelectionLRT.bf), but I don't see how to prepartition the tree for such condition. What is the format to prepartition the tree? Any help would be greatly appreciated, Bests, Albert. |
Title: Re: "Free-ratios"-like analysis in PAML Post by Simon on Jul 26th, 2005 at 8:18am
Dear Albert,
You can easily test a free ratio model for a 4 species alignment using the graphical interface. Open the data (using the File menu), select the sequences, generate a partition of these sequences (Data>Selection -> Partition), toggle the partition type to 'Codon', add your tree, choose a codon substitution model, then choose the 'local' option in the 'Parameter type' section. You can then optimize the likelihood function. The nice thing about this approach is that you can then easily perform likelihood ratio tests for differences in dN/dS, etc. Best Simon |
Title: Re: "Free-ratios"-like analysis in PAML Post by avilella on Jul 26th, 2005 at 10:10am
My datasets are typically of very long seqs (MBs) for few species, and usually the runs of the analyses take a lot of time (hours/days).
If I can pre-set the parameters of the analysis in a params.txt file, then I can batch the jobs to a server computer and run them like: ./HYPHYMP < params.txt > stdout.txt In my previous tests, I couldn't find a way to "plug" the results of the batch part to the "Analysis->Results" part, in the GUI, that you describe. Is this possible? Then, ideally, I would be able to have the longest part of the analysis done as a batch job and then use the resulting data in the GUI for the "Analysis->Results" part. Thanks in advance, Albert. |
Title: Re: "Free-ratios"-like analysis in PAML Post by Sergei on Jul 26th, 2005 at 11:19am Quote:
This is indeed possible. 1). Add the following lines to the end of params.txt (square bracketed stuff are my comments and should not be included in the file) y [In response to "Continue with result processing?"] 2 [Save Results] 7 [Save all the components of the analysis in a self-contained HyPhy batch file.] File Name to Store Results in n [In response to "Continue with result processing?"] 2). Call ./HYPHYMPU CPU=xx -p <params.txt > stdout.thx where xx is the number of processors on your system. 3). Open the result file made by the first step (with the name you had specified) in the GUI version (File->Open->Open Batch File) and use the Result processing modules. HTH, Sergei |
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