[Biopython-dev] [Bug 2961] New: Adding undocumented file format switches to MUSCLE wrapper

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2961

           Summary: Adding undocumented file format switches to MUSCLE
                    wrapper
           Product: Biopython
           Version: Not Applicable
          Platform: PC
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk


As discussed on the mailing list, and confirmed with MUSCLE author Robert
Edgar,
there are a number of useful command line arguments for things like PHYLIP
output
(both interlaced and sequential) which the Bio.Align.Applications wrapper does
not support. See:
http://lists.open-bio.org/pipermail/biopython/2009-December/005881.html

We should add these.


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