[Biopython] Phylogenetic trees with biopython?

[Italo Maia]

I'll try pycongent too but, for now, i'll leave it with clustalw for being
the fastest way for me to get it done. Anyway, the "clustering" option for
ClustalCommandline seems to be buggy. In the _Option parameter, equate
should be set to True, in order for it to work.

2009/9/2 David Winter <winda002 at student.otago.ac.nz>

>
>  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
>



-- 
"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!
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