[Biopython] MuscleCommandline and phyiout

[John Cumbers]

Hello,

I'm using the MuscleCommandline wrapper and I'm having trouble getting the
Phylip interleaved output format.  For the Muscle command line I would type
"muscle -in myinputfile -phyiout myoutputfile" and this command in python:
cline = MuscleCommandline (input=output_file_name_FASTA,
out=output_file_name_aligned)

But for phyiout, this doesn't work:
cline = MuscleCommandline (input=output_file_name_FASTA,
phyiout=output_file_name_aligned)
returning: ValueError: Option name phyiout was not found.

I tried to lookup the possibilities here:
http://www.biopython.org/DIST/docs/api/Bio.Align.Applications._Muscle.MuscleCommandline-class.html

but couldn't find them, any help appreciated,
cheers,
John


John Cumbers, Ph.D Candidate
NASA Ames Research Center
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