GDE-L is a workbench tool that is easily adapted to any small-sized sequence, in the range of 10-20 Kb. The development and application of scripts is a novel approach that makes it easier to add, maintain and update sequence databases. Scripts provide the user with the expertise needed to maintain and/or develop detailed organism-specific interfaces.
The GDE for Linux main page contais more information on GDE-L use for sequence analysis.
Genetic Data Environment (GDE) License and Registration:
Genetic Data Environment (GDE) was originally developed at Harvard by Steven Smith. The original version can be downloaded from the ftp site: ftp://megasun.BCH.UMontreal.CA/pub/gde/ The Genetic Data Environment: An Expandable GUI for Multiple Sequence Analysis by S. Smith.
GDE licence is in the documentation (doc) directory in the distribution and can be read here.
Download Software:
GDE for Linux executables:
- GDElinux.tar.gz (2.4 Mb )
- RedHat (rpm): xview-3.2p1.4-6.i386.rpm (0.5 Mb) , xview-clients-3.2p1.4-6.i386.rpm (0.4 Mb)
- Debian (deb): xviewg_3.2p1.4-9.deb (0.6 Mb) , xviewg-dev_3.2p1.4-9.deb (0.9 Mb)
- tar.gz (others distributions): xview_3.2p1.4.tar.gz (3.1 Mb)
The main advantage of the GDE is that menus for other bioinformatics software can be created, by editing a unique menu control file (.GDEmenus), allowing the user to run the desire software from the GDE graphical interface.
It is necessary to download and install the software above for using GDE for Linux:
| Software | Web Site | RedHat (rpm) download | Debian (deb) download | tar.gz (other distributions) |
| Readseq Clustalw Phylip Treetool BLAST- |
Readseq
web site Clustalw web site Phylip web site Treetoolweb site Blast web site |
readseq-0.0-2.i386.rpm
clustalw-1.7-8.i386.rpm phylip-3.5c-4.i386.rpm treetool-2.0.2-2.i386.rpm ncbi-tools6-6.0-4.i386.rpm blast2-6.0.2-2.i386.rpm |
readseq_0.0-2.deb
clustalw_1.7-7.deb phylip_3.573c-1.deb treetool_2.0.2-1.deb ncbi-tools6_6.0.2-1.1.deb blast2_6.0.2-1.1.deb |
Many bioinformatics software had already been integrated in the GDE menus, . See the list of software and menu files for GDE.
PERL scripts for adding
sequence database, aligments,
and
web resources:
- installBLASTDBDNA.pl - Script for adding a new DNA blast formatted database in the GDE menu
- installBLASTDBPROT.pl - Script for adding a new protein blast formatted database in the GDE menu
- newDATASET.pl - Script for adding a sequence dataset (alignments) in the GDE menu
- newURL.pl - Script for adding a new web resource in the GDE menu
- Installation instruction.
- Questions and Answers (Troubleshooting).
- How to cite GDE for Linux in a publication.
- GDE for Linux basic functions tutorial (alignment, translation, phylogenetic tree construction, etc.)
- How to integrate bioinformatics software editing the menu file (.GDEmenus) [PDF file]
- GDE documentation and tutorials online.