RE: [Gusdev-gusdev] GUS 3.5 Release

[davila <da...@io...>]

Hi Aaron, Mike,

Indeed, comparative genomics will receive major benefit from =
phylogeny/evolutionary analyses...=20

Could you share any further info/details on your CDAT initiative ?... =
sure, tables should support (help to differentiate) gene trees from =
species trees, (phylogenomics ?) etc.

I hope to be able to provide a draft schema for this next week or so, =
hope it is not too late...=20

Cheers, Alberto



-----Original Message-----
From:	Aaron J. Mackey [mailto:am...@pc...]
Sent:	Wed 1/26/2005 2:22 PM
To:	gusdev-gusdev
Cc:=09
Subject:	Re: [Gusdev-gusdev] GUS 3.5 Release

On Jan 26, 2005, at 11:13 AM, Michael Saffitz wrote:

> GUS doesn't currently support phylogeny/evolutionary data, but are=20
> very open to adding it to GUS.  Do you have a schema (rough or=20
> otherwise) in mind?

I think the upcoming comparative genomics efforts here (and elsewhere)=20
will certainly require support for evolutionary analyses.  I would=20
encourage those doing the schema design to consider both multiple=20
sequence alignments and trees (including associated bootstraps,=20
likelihood, branch lengths, etc) as experimental results that may be=20
computed in many different fashions.  I.e. don't fall into the trap of=20
the "one true tree", because it doesn't exist.

I'd be very interested to be involved in this effort, and to give a=20
talk on my own phylogenetic sequence database (CDAT) for consideration=20
as one possible schema to mimic.

-Aaron

--
Aaron J. Mackey, Ph.D.
Dept. of Biology, Goddard 212
University of Pennsylvania       email:  am...@pc...
415 S. University Avenue         office: 215-898-1205
Philadelphia, PA  19104-6017     fax:    215-746-6697