[Biopython-dev] Bio.Phylo.Applications?

[Peter]

Hi Eric et al,

We have started a collection of command line tool wrappers for
multiple sequence alignments under Bio.Align.Applications, so I was
thinking about where to put wrappers for phylogenetic tree command
line tools. How does Bio.Phylo.Applications sound (following the same
structure as the Bio.Align.Applications module). The kind of things I
am thinking about include:

QuickTree (neighbour joining, NJ)
http://www.sanger.ac.uk/resources/software/quicktree/

QuickJoin (NJ)
http://www.daimi.au.dk/~mailund/quick-join.html

RaxML (maximum likelihood, ML),
http://icwww.epfl.ch/~stamatak/index-Dateien/Page443.htm
[We should talk to Biopython contributor Frank Kauff as he uses this
with Python]

And so on. Plus pointers in the documentation to the EMBOSS module for
PHYLIP tools.

Peter