[Bioperl-l] dn/ds code from PAML howto not working

Stefan Kirov stefan.kirov at bms.com
Tue Mar 27 17:13:03 EDT 2007


Amir Karger wrote:
> A client of mine stole the pairwise Ka/Ks code from the "Running PAML
> from within Bioperl" section of the PAML HOWTO. It mostly seems to be
> running fine. However, when we say
> 	$result = $parser->next_result;
>
> we get an undef $result. 
>
> 1) Is there something I can look for in the output files to show me
> whether it's a problem with Bioperl itself (Never!) or with CODEML?
>
> 2) Is there a previously known issue with Bioperl's incorrectly reading
> such files? Bio::Root::Version says it's 1.5, by the way.
>
> 3) Something else I haven't thought of?
>
> Thanks,
>
> Amir Karger
> Research Computing, Life Sciences Division
> Harvard University
>
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>
>   
Do you get a message saying you have no sites? Have you looked at the 
alignments?
Stefan


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