[Biopython] Phylogenetic trees with biopython?

[Peter]

On Tue, Sep 1, 2009 at 7:17 AM, David
Winter<winda002 at student.otago.ac.nz> wrote:
>
>> Is it possible to create phylogenetic trees with biopython alone or i'll
>> have to "phylip things up" a little? Phylip doesn't seem to allow
>> execution with options, as blast does, per example, and that really
>> botters me. :
>
> Hi Italo,
>
> It depends on what exactly you want to do. If you want to run phylip
> programs as part of a biopython script then there are classes in
> Emboss.Applications for building up command lines to call the EMBOSS
> versions of enough of the phylip packages to make bootstrapped distance or
> parsimony trees. That would mean installing EMBOSS if you don't already have
> it but it makes automating phylip much, much easier.

Yes - we definitely recommend the EMBOSS versions of the PHYLIP
tools because they support command line arguments, and the originals
don't.

> Those should let you define all the relevant arguments (if they don't it's
> easy to add them, so shout out) but they are for the 'old' versions of
> phylip, I'm sure you can still get the EMBOSS versions of  these from their
> site  but  there are also 'new' versions which are meant to be a little
> faster but take different arguments (so the existing classes won't help
> you). I put up a branch on github which has classes for the new versions as
> well as for PhyML in Bio.Phylo here:
> http://github.com/dwinter/biopython/tree/phylo

Yes, as David points out, Bio.Emboss.Applications has wrappers for the
"old" versions from PHYLIP 3.572 (whose EMBOSS names start with e):
http://emboss.sourceforge.net/apps/release/6.1/embassy/phylip/

We should add the "new" versions from PHYLIP 3.6  (whose EMBOSS
names start with f):
http://emboss.sourceforge.net/apps/release/6.1/embassy/phylipnew/

David - I would prefer we also put your new wrappers in
Bio.Emboss.Applications, and would be happy to look at adding
those to CVS now that Biopython 1.51 is out (I had forgotten
about them actually - so thanks for the reminder).

Peter