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

[Scott Markel]

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

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Scott Markel, Ph.D.
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