[Bioperl-l] Error calling alignment method

[Jason Stajich]

> ------------------------------------------
> 
> I think the codon alignment is being proberly constructed by the method aa_to_dna_aln, as I can do a Dumper printing of it. So the problem must be in the PAML codeml wrapper not properly recognizing the codon alignment. Could it be related to the alignment format (PAML runs on PHYLIP formatted files)?
The writing out in phylip format is taking care of by the factory - you are passing in an alignment object so that is not typically the problem.

I would repeat Dave's idea that you just dump the codon alignment file out and you run PAML manually with it.  The parsing error sounds like there are problems when running PAML and you may want to check that you don't have stop codons in your alignment.  It looks like your CDS file has stops as the last codon so if you drop those last 3 bases, how does it work?

> Cheers,
> Lorenzo
> 
> 
> 
> -- 
> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
> Lorenzo Carretero Paulet
> Institute for Plant Molecular and Cell Biology - IBMCP (CSIC-UPV)
> Integrative Systems Biology Group
> C/ Ingeniero Fausto Elio s/n.
> 46022 Valencia, Spain
> 
> Phone:  +34 963879934
> Fax:    +34 963877859
> e-mail: locarpau at upvnet.upv.es
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