[Bioperl-l] Fwd: PAML through BIOPERL - parsing error

Jason Stajich jason at bioperl.org
Mon Jun 23 11:02:56 EDT 2008

You'll have to report what version of BioPerl and PAML you are using,  
only certain versions work together because the report output from  
PAML changes in each version.  We have tried to fix it for PAML4 in  
the latest code in SVN and I believe PAML 3.15 should work with what  
is in 1.5.2 release of BioPerl  but I'm not sure.

Please direct your questions to the mailing list to insure someone  
has a chance to look at it.


Begin forwarded message:

> From: Tannistha <tannistha3 at yahoo.com>
> Date: June 22, 2008 10:43:41 PM PDT
> To: jason at bioperl.org
> Subject: PAML through BIOPERL - parsing error
> Reply-To: tannistha3 at yahoo.com
> Hi Jason,
> I am using PAML through BIOPERL. My input in multiple CDS sequence.  
> I am getting an error while parsing my codeml result.
> The error is:
> Use of uninitialized value in pattern match (m//) at /usr/lib/perl5/ 
> site_perl/5.8.5/Bio/Tools/Phylo/PAML.pm line 615, <GEN2> line 90.
> Please suggest how to eliminate this error.
> Thanking you
> Regards
> Dr. Tannistha Nandi
> email: tannistha3 at yahoo.com

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