[Biopython] Phylogenetic trees with biopython?

[Italo Maia]

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 : /) 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.

ps: i just made a simple frontend for blast, formatdb, clustalw and muscle.
Right now i'm going to add phylogenetic trees, then, i'm finished. It's my
graduation thesis, by the way.

2009/9/1 David Winter <winda002 at student.otago.ac.nz>

>
>  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
>>
>
> Hi Peter,
>
> I'd almost forgotten about them myself! I only put them in their own module
> because I had the PhyML wrapper as well and that's not an EMBOSS
> application.
>
>  I suspect a wrapper for PhyML is probably not going to be widely useful (a
> normal run lasts at least several hours and most people will want to look
> over their alignments by eye before they set it off). So I'll move the
> phylip ones into Emboss.Applications and gather a few thoughts about other
> phylogenetic software including PhyML and see what the dev list thinks about
> them.
>
> david
>
>
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>



-- 
"A arrogância é a arma dos fracos."

===========================
Italo Moreira Campelo Maia
Ciência da Computação - UECE
Desenvolvedor WEB e Desktop
Programador Java, Python
Ubuntu User For Life!
-----------------------------------------------------
http://www.italomaia.com/
http://twitter.com/italomaia/
http://eusouolobomal.blogspot.com/
===========================