[Bioperl-l] population genetics

[Matthew Hahn]

There's now a composite genotypic LD method in Bio::PopGen::Statistics.

The genotypic method doesn't require you to infer haplotypes using an 
EM or likelihood method, it just works from diploid data.  It has 
slightly less power because of this.  I'm sure a statistic for 
gametic LD would be appreciated.


cheers,
Matt



>----- Forwarded message from Paulo Almeida <paulo.david at netvisao.pt> -----
>     Date: Tue, 27 Apr 2004 15:39:56 +0100
>     From: Paulo Almeida <paulo.david at netvisao.pt>
>Reply-To: Paulo Almeida <paulo.david at netvisao.pt>
>  Subject: Re: [Bioperl-l] population genetics
>       To: Pedro.X.Gomez-Fabre at gsk.com
>
>     I don't know about LD (linkage disequilibrium?) and EM models on
>bioperl, but there are probably implementations for various applications
>of it on R statistics software (I know there is for QTL analysis). I
>recently came across this module to control the R interpreter from Perl:
>
>      http://search.cpan.org/~gmpassos/Statistics-R-0.02/lib/Statistics/R.pm
>   
>     Seeing that R is also Open Source, it might be interesting to use it
>with BioPerl.
>
>     -Paulo Almeida
>
>Pedro.X.Gomez-Fabre at gsk.com wrote:
>
>>Hi all,
>>
>>I would like to go for an LD viewer and infer haplotypes based on EM
>>model. I was wondering is some on the list is doing something like that.
>>
>>Cheers
>>Pedro.
>>
>
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