[Biopython] Phylogenetic trees with biopython?

[David Winter]

> 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.

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

Hope that helps you out,
David