[Biopython-dev] Phylip interface questions

[David Winter]

Hi Marshall,

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:

http://github.com/dwinter/biopython/tree/phylo

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.)


Cheers,
David