[Biopython] Phylogenetic trees with biopython?

[Italo Maia]

I want to use them to study evolution. Maybe guide some protein modelling.
Would you suggest a better use?

2009/9/1 Paulo Nuin <nuin at genedrift.org>

> ClustalW trees are extremely "simple" and only can be generated with
> Neighbour Joining. Also they are not based on the final sequence alignment
> created by the program but as a guide for the alignment itself. They have a
> huge probability of being "wrong" or not representing the actual
> relationships. It will heavily depend on the the type, distance and
> differences among the sequences you are using.
>
> Do you need trees for what?
>
> Paulo
>
>
>
>
> On 1-Sep-09, at 10:37 PM, Italo Maia wrote:
>
>  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
>>>
>>>
>>> _______________________________________________
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>>> 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/
>> ===========================
>>
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>> 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/
===========================