[Bioperl-l] Convert Fasta to Phylip

[Jason Stajich]

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/