[Biopython] MuscleCommandline and phyiout

[Peter]

On Tue, Dec 1, 2009 at 9:23 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Tue, Dec 1, 2009 at 7:10 AM, John Cumbers <johncumbers at gmail.com> wrote:
>> 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"
>
> What version of MUSCLE do you have? v3.7 doesn't mention this
> option in the command line help, nor does the current manual:
> http://www.drive5.com/muscle/muscle.html

It looks like an undocumented option, much like -phyi (which I guessed)
for PHYLIP interlaced and -phys for PHYLIP sequential. These match
the documented format options (e.g. -msf, -html, -clw and -clwstrict).
i.e. You can use this:

"muscle -in myinputfile -phyi -out myoutputfile"

I think we should ask the MUSCLE author which of these
undocumented arguments are actually supported rather than
adding them all.

Peter