GDE Linux Download

An integrated linux environment for bioinformatics and evolutionary analysis based on the Genetic Data Environment (GDE).

Cite the usage of GDE by citing the following paper
de Oliveira T, Miller R, Tarin M, Cassol S. An Integrated Genetic Data Environment (GDE)-Based LINUX Interface for Analysis of HIV-1 and Other Microbial Sequences. (2003) Bioinformatics, 19(1): 153-4.

Download Software:

GDE for Linux executables:

Xview libraries necessary for GDE for Linux:  Bioinformatics software integration with GDE for Linux: 
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
Documentation available:



Page last updated by Tulio de Oliveira.