[Bioperl-l] Bio::Align::DNAStatistics extension?

[Jason Stajich]

Richard -

Yes please - in process of doing pi and theta calculations, etc in there
as well.

-jason

On Tue, 15 Jul 2003, Richard Adams wrote:

> Hello,
>         I've written a module that is basically a simple implementation
> of the Nei-Gojobori method for calculating
>         the ratio of synonymous:nonsynonymous mutations in a DNA
> alignment of a coding sequence.
>
>         At present it just  calculates the z-score and intermediate
> results for pairwise sequence comparisons using the Jukes-Cantor
> nucleotide substition model
>         or for multiple sequence comparisons by bootstrapping. The idea
> is that you can just put in a Bio::SimpleAlign object or
> alignment slice and get some idea of the extent of positive/negative
> selection easily.
>
>     Just looking at the        the Bio::Align::DNAStatistics module,
> would it be of any interest to integrate some of these methods available
> in that module, or are they too specific for BioPerl?
>
> Richard
>
> --
> Dr Richard Adams
> Bioinformatician,
> Psychiatric Genetics Group,
> Medical Genetics,
> Molecular Medicine Centre,
> Western General Hospital,
> Crewe Rd West,
> Edinburgh UK
> EH4 2XU
>
> Tel: 44 131 651 1084
> richard.adams at ed.ac.uk
>
>
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu