[Biopython] Phylogenetic trees with biopython?

[David Winter]

> Thank you everyone for your answers. I was about to give up and run my 
> own wrappers over phylip(emboss for mey ubuntu is too old : /)
It shouldn't matter how old your emboss is - I think there are phylip 
versions for every release of EMBOSS here:
ftp://emboss.open-bio.org/pub/EMBOSS/old/

EMBOSS doesn't come with the phylip programs by default, you need to 
download them independently. There are no binaries for ubuntu but 
they're very easy to compile (if I can do it...) -  you do need the 
EMBOSS sources though.
> when i just found out that clustal can create phylogenetic trees too. 
> On commandline, with the options 4,1 and 4, i just made a tree here, 
> from a .aln file generated with clustalw. Does anyone dislike this 
> approach? Seems like easy/fast/efficient enough for me.
>
As Paulo says this might be easy/fast/efficient but there is no promise 
it will be accurate/powerful/useful ;). If you want to do it with 
existing biopython tools then I think phylip is probably going to be the 
way to go.

You might also want to look at PyCogent which has controllers for some 
other phylogeny programs:
http://pycogent.sourceforge.net/examples/phylogeny_app_controllers.html

(I have no experience using those, so can't tell much about them)

Cheers,
David