[Bioperl-l] how to go from AlignIO to Variation ?

[Albert Vilella]

Hi Jorge,

(good to see an ex-EBI in the bioperl-ml :-) )

You can use the method aln_to_population in Bio::PopGen::Utilities:

my $pop = Bio::PopGen::Utilities->aln_to_population($aln);

http://www.bioperl.org/wiki/HOWTO:PopGen#Allele_data_from_Alignments_using_Bio::AlignIO_and_Bio::PopGen::Utilities

Cheers,

    Albert.

On Wed, Mar 19, 2008 at 3:32 PM,  <Jorge.DUARTE at biogemma.com> wrote:
> Dear Bioperl-users,
>
>  could someone give me a hint on how to find SNPs in alignments using
>  bioperl objects ?
>
>  I found several modules capable of representing Sequence Variations,
>  but could not understand how to go from an "Align" object to a "Variation"
>  object.
>
>  Any help would be much appreciated,
>
>  Thanks,
>
>  Jorge.
>
>  ---
>  Jorge Duarte
>  Bioinformatics Software Engineer
>  BIOGEMMA
>  Z.I. Du Brézet
>  8, Rue des Frères Lumière
>  63028 CLERMONT FERRAND Cedex 2
>  FRANCE
>  Tel : +33 (0)4 73 39 60 73
>  Fax : +33 (0)4 73 39 60 71
>  E-mail : jorge.duarte at biogemma.com
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