[Bioperl-l] Bio::Tools::Run::Alignment::Clustalw & Phylogenetic trees

[Steven Cannon]

On Monday, May 27, 2002, at 11:02 AM, bioperl-l-request@bioperl.org 
wrote:

> Message: 3
> From: "Elia Stupka" <elia@fugu-sg.org>
> To: "Jason Stajich" <jason@cgt.mc.duke.edu>,
>        "Eduardo Arino de la Rubia" <arino@arino.net>
> Cc: <bioperl-l@bioperl.org>
> Subject: Re: [Bioperl-l] Bio::Tools::Run::Alignment::Clustalw & 
> Phylogenetic trees
> Date: Mon, 27 May 2002 03:26:21 +0800
> Organization: IMCB
>
>> What would be helpful is to describe some use cases for what you would
>> like to learn from the trees.  There have been some talk of building
>> ortholog predictions - the fugu guys may have already started on the 
>> alg
>> building?
>
> Sure if we get use cases we'd be interested in exercising them on the
> pipeline.... we haven't started the algorithm part at all, not even 
> sure if
> right now it will be a priority any time soon since we want to focus on
> non-coding sequence for a while....
>
> Elia
>

I have been working on a phylogenetic / genome position / orthology 
pipeline, but it is quite a big cumbersome thing that works on whole 
genomes. Will probably be a while before it is cleaned up for general 
use. But I would be interested in talking with others who are working on 
similar projects.

Steve Cannon