[Biopython] MuscleCommandline and phyiout

[Peter]

On Tue, Dec 1, 2009 at 9:52 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>
> 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.

Robert Edgar agreed the documentation was out of sync, and has
confirmed these are safe arguments to include in our wrapper.

Peter