[Bioperl-l] Convert Fasta to Phylip

[Jason Stajich]

AlignIO does both of them.

you need to say
-interleave => 0
for phylip format as non-interleaved (although most programs will  
handle both I think).

AlignIO::nexus
writes files fine for PAUP, I use it all the time.

I have to pare down seq ids so they're unique in phylip format for  
PAML,PHYML,MB,PROTML.
there are a couple of options you need to apply to make MB compliant  
nexus files (plus make sure there are no dashes in your seqids).


I store everything in fasta MSA format and then convert to phylip/ 
nexus as necessary since it is easy to manage and will let you have  
long seq descriptions (I know selex/stockholm will too but fasta  
comes directly out of MUSCLE too).

-jason
On May 28, 2005, at 10:10 PM, Alberto Davila wrote:

> Hi all,
>
> Talking about format conversion, I recently needed to deal with  
> Phylip, Paup and PhyML (http://atgc.lirmm.fr/phyml/) and  
> unfortunately it is still a pain to convert files among them.  
> ClustalW can generate an output in Phylip interleave format, but  
> not the non-interlevae one. Seqret (Emboss) claims to be able to  
> convert between those 2 Phylip formats, but did not work to me.  
> Would be there any Bioperl module to dela with that ? or plans to  
> expand the SeqIO module to deal with both Phylip formats and Paup  
> (nexus) ?
>
> Thanks, Alberto
>
> At 10:54 25/5/2005, you wrote:
>
>> You should send an example of the file you are trying to convert. It
>> works fine for me and you can see a test file in t/data/testaln.fasta
>>
>> -jason
>>
>> On May 25, 2005, at 5:58 AM, Ferdinand Marlétaz wrote:
>>
>>
>>> Hi,
>>>
>>> I'd like to ask something : I have a fasta file with pieces of
>>> manually controlled alignement (with - for "Gaps") and I've tried
>>> to read it with AlignIO ( just like my $in  = Bio::AlignIO->new(-  
>>> file => $inputfilename , '-format' => 'fasta');    ) in order to
>>> convert it to phylip formatted sequence but... it reply me MSG: Got
>>> a sequence with no letters in it cannot guess alphabet [] . So, I'd
>>> like to understand how to convert a fasta alignement containing
>>> file into a phylip file for phylogeny.
>>> Thank you very much !
>>>
>>> Cheers
>>>
>>> Ferdi
>>>
>>> _____________________________
>>> Ferdinand Marlétaz
>>> Evolution et phylogénie des métazoaires
>>> UMR 6540 DIMAR
>>> Rue Batterie des Lions
>>> 13007 MARSEILLE
>>> Tel. 04 91 04 16 54
>>> Port. 06 30 35 58 49
>>> Mail. Ferdinand.Marletaz at ens-lyon.f
>>>
>>
>> --
>> Jason Stajich
>> jason.stajich at duke.edu
>> http://www.duke.edu/~jes12/
>>
>
>
>

--
Jason Stajich
Duke University
http://www.duke.edu/~jes12/