[Biopython] Phylogenetic trees with biopython?

[Italo Maia]

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/
===========================