[Biopython] Phylogenetic trees with biopython?

[Paulo Nuin]

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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>
>
>
> -- 
> "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/
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> http://eusouolobomal.blogspot.com/
> ===========================
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