GDE on the DECstation

Steven Smith smith at phylo.life.uiuc.edu
Wed Mar 25 12:12:40 EST 1992

We are getting ready to ship GDE2.0 to beta testers on the DECstation.
Interested parties should send email to smith at nucleus.harvard.edu.
We are limiting this beta release to no more that a dozen sights,
with priority given to those groups doing software development.
We hope to ship GDE2.0 proper next month.

The Genetic Data Environment (GDE) is a set of programs for sequence alignment
assembly and analysis. The GDE currently runs on SUN and DEC workstaions using
OpenWindows 2.0/3.0 or MIT X11R4/R5.  The programs use an expandable user
interface which allows the addition of external analysis functions without
any rewriting of code.  Analysis functions can be written in any language
('C',Fortran, Pascal Basic, shell scripts), and can be seamlessly merged
into the systems menu/dialog box interface.

The system supports several data types, nucleic and amino acid sequences,
text, and masking sequence, and several forms of color highlighting.  The
system can handle enormous alignments limited only by the amount of virtual
memory on your workstation.

Sequences can be edited under several levels of protection, as well
as by aligned groups.  The system has several external analysis
functions included for such things as automated alignment, searching,
homology recognition, and phylogenetic analysis.

Thanks to the generous contributions from many authors, we are including
in this release are:

Blast				Basic Local Alignment Tool
FastA				Homology searching

Phylip				Complete Phylogenetic Analysis package
DeSoetes method			Phylogenetic tree calculation.
TreeTool			Phylogenetic tree manipulation

ClustalV			Multiple sequence alignment
CAP				Contig Assembly Program using a DP

ReadSeq				File conversion

MFOLD				RNA Secondary Structure
LoopTool			Secondary Structure Display

Plus Email services for homology searched, database access, and gene
recognition, and further programs for sequence management.

The programs are not in the public domain, but are and will continue to be
available for free.  This is done to protect the interests of the individual
contributing authors.  Distribution will include full source code, and binaries
along with a users manual.

Steven Smith
Director of Computation
Harvard Genome Lab

smith at nucleus.harvard.edu

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