[Biopython] MuscleCommandline and phyiout

[John Cumbers]

Many thanks Peter,
Sorry for delayed reply, I filter this list and forgot to check the folder
:)
Best wishes,
John

John Cumbers, Ph.D Candidate
NASA Ames Research Center
Mail Stop 239-20, Bldg N239 Rm 373 Moffett Field, CA 94035, USA.
cell +1 (401) 523 8190, office +1 (650) 604-1914, fax +1 (650) 604-1088

Graduate Program in Molecular Biology, Cell Biology, and Biochemistry
Brown University, Box G-W Providence, RI, 02912, USA


On Tue, Dec 1, 2009 at 11:19 AM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> 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
>