[Biopython-dev] Phylip interface questions
winda002 at student.otago.ac.nz
Tue Jul 28 01:56:46 UTC 2009
I am wondering if there is already an interface to the Phylip programs
in biopython. I am pretty sure there is not, but I wanted to ask
before doing a chunk of work on one. I know that AlignIO can read and
write the phylip alignment files, but I think that is it.
Assuming such a thing doesn't already exist, I will write some
functions for calling various combinations of programs in phylip to
make some common tasks easier. Mostly this will use the pexpect module.
I wrote a few for my own use (I presumed no one else was doing stuff
like this) which I've now uploaded as module (Bio.Phylo) here:
They are for the 'new phylip' version ('f' prefixed not 'e') in
EMBOSS's 'embassy' packages (which take different arguments than the
classes already in the EMBOSS module...). They also depend on the cool
stuff that Brad and Peter have done for applications in biopython
1.51. Hopefully they will cover some of the same ground that you want
to, or at least prevent you having to start from scratch.
(There's also support for PhyML which is based on phylip's dnaml but
it much faster.)
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