[Bioperl-l] PAML parser failed for PAML 4.3b and 4.1

Chris Fields cjfields at illinois.edu
Wed Dec 23 16:19:48 EST 2009

Well, not completely unexpected, but very frustrating nonetheless.  Changes to PAML output have broken in just about every PAML parser revision.  Not sure when this will be addressed unfortunately, my hope is sooner than later.

Can you file a bioperl bug report for this?  It's the best place to keep track.



On Dec 23, 2009, at 12:36 PM, pkuonline wrote:

> Hi Everyone,
> I used the latest Bioperl build, http://www.bioperl.org/DIST/nightly_builds/bioperl-live.tar.gz and tried to parse CODEML result. I searched the mail list and found current PAML parser is compatible with PAML 4.3a, http://lists.open-bio.org/pipermail/bioperl-l/2009-November/031602.html. However, recently, Ziheng Yang updates his PAML to 4.3b. I found the parser does not work. More strangely, I tested it on the old PAML 4.1 result and also failed. 
> I attached my CODEML outputs here to see whether you guys have some idea. 
> Many thanks ahead!
> Best regards,
> -------------------------------------------------------------
> Yong Zhang
> Ph.D, Research Scholar
> Manyuan Long's Lab
> University of Chicago<rst4.1><mlc4.1><mlc4.3b><rst4.3b>_______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

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