[Bioperl-l] why does Bio::Tools::Run::Hmmer return a SearchIO object for hmmalign?

Scott Markel smarkel at scitegic.com
Tue Apr 12 20:23:32 EDT 2005

I'm curious as to why Bio::Tools::Run::Hmmer returns a
SearchIO object when the program is hmmalign.  I would
have expected an AlignIO object since the result of an
hmmalign execution is a Stockholm formatted alignment file.

I expect that I'm missing something obvious, but I don't
see it.  An online search, including the mailing list
archive, didn't help.


Scott Markel, Ph.D.
Principal Bioinformatics Architect  email:  smarkel at scitegic.com
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