[Bioperl-l] Getting clustalw alignments in a form codeml can use

Julian M Catchen catchen at cs.uoregon.edu
Tue Jun 22 19:23:29 EDT 2004


Can someone help me with the following problem? I am aligning sequences using  
clustalw and then storing the text strings from the alignment individually in  
a database. I want to then pull these sequences from the database and feed  
them to PAML::codeml, but I can't figure out what object to load them into  
that codeml will understand. I can see how to add them to Bio::Seq objects,  
but what do I do with them after that? It appears to me that codeml requires  
a Bio::AlignI object in order to execute.

I have previously written the clustal alignments out to a file and then used  
an Bio::AlignIO object to read them in and give me my Bio::AlignI object for  
codeml, but I would like to do this entirely within the database and I would  
prefer not dumping a verbatim clustal file into the database. Anyone have any  

Thanks in advance for any help,


Julian M Catchen
Computer and Information Science | catchen at cs.uoregon.edu
229 Deschutes Hall               | (541) 346-1382
University of Oregon             | http://www.cs.uoregon.edu/~catchen/

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