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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl Methodology Questions >> How to >> Using HyPhy batch files with partition data http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1288802933 Message started by pborrego on Nov 3^rd, 2010 at 9:48am

Title: Using HyPhy batch files with partition data
Post by pborrego on Nov 3^rd, 2010 at 9:48am

Dear Sirs,
SBP analysis in Datamonkey identified a single recombination point in my alignment (95 sequences).
Since REL analysis is impossible in Datamonkey for this number of sequences, I will have to use the dNdSRateAnalysis.bf in HyPhy.
(I'm also interested in other batch files like AnalyseCodonData.bf, TestBranchdNdS.bf, etc...).
I know how to make a partitions in HyPhy and add trees to each partition, but:
1 - How can I make a file that includes both alignment+trees in a way that in future batch file analysis (for REL or global dN/dS) it uses both information, i.e. Partition1+tree1 and Partition2+Tree2??
2 - For this purpose, do I have to define the partition type as codon or can I leave it as nucleotide? I'm asking this because the SBP is in the middle of a codon, and to keep sequences in frame I would have to exclude that codon from both partition, i.e. 1 - 228, 232 - 369.

Thank you very much,

Pedro Borrego
Portugal

Thank you

Title: Re: Using HyPhy batch files with partition data
Post by Sergei on Nov 3^rd, 2010 at 10:42am

Hi Pedro,

You should look under the Selection/Recombination rubrik in HyPhy standard analysis for the selection of tools that support multiple partitions. Generally, you can combine everything in a single NEXUS file following the format output by GARD (attached below). HyPhy will automatically adjust the location of the breakpoint to preserve reading frames, by moving it to the nearest codon boundary.

Sergei

http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?action=downloadfile;file=example_nex.zip (3 KB | )

Title: Re: Using HyPhy batch files with partition data
Post by pborrego on Nov 3^rd, 2010 at 1:04pm

Great!!
Thanks for your help. I was in the right track with the file I had prepared, but I didn't know about the methods inside the Selection/Recombination rubrik.
I've just started to run the dNdSRateAnalysis_MP.bf analysis. Hope everithing will be ok.
Thank you.

Pedro Borrego
PORTUGAL

Title: Re: Using HyPhy batch files with partition data
Post by pborrego on Nov 3^rd, 2010 at 2:28pm

By the way, I'm sorry to bother you again but the output from the REL analysis in Datamonkey give the posterior probability for positive selection (dN>dS) for each positively selected site. How can I get that value from the HyPhy REL analysis?
Beside Bayes Factors, those dNdSResultProcessor.bf compute posterior probabilities using the .marginals file?

Thank you,

Pedro Borrego
PORTUGAL