[Biopython] Phylogenetic trees with biopython?

[Italo Maia]

Solved with a terrible ugly forloop.

*for* par *in* self.cline.parameters:
names = getattr(par, 'names', None)
*if* names *is* not None:
*if* "-clustering" *in* names:
par.equate=True

And clustalw can generate trees in phylip format, which is good news for me!
Thank you guys!
When i grab my hands in pycongent, i'll post something.
And, by the way, emboss didn't seem to work fine in my ubuntu, even tough
the package is in the repository. If i write "emboss" in the console, it
won't work. @.o




2009/9/2 Italo Maia <italo.maia at gmail.com>

> ps: is there a work around, for this "wannabe" bug?
>
> 2009/9/2 Italo Maia <italo.maia at gmail.com>
>
> 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!
>> -----------------------------------------------------
>> http://www.italomaia.com/
>> http://twitter.com/italomaia/
>> http://eusouolobomal.blogspot.com/
>> ===========================
>>
>
>
>
> --
> "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/
> ===========================
>



-- 
"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/
===========================