Download from this page some usefull tools

GenBank2Treedyn

Extract annotations from GenBank files for:

• More convenient alignments and phylogeny (replace def line of  fasta file by GI number)
• Extremely powerfull annotations of phylogenetic trees with TreeDyn.

author: Richard Christen, François Chevenet
License: GNU General Public License (GPL)
Natural Language: English
Operating System: OS independent
Programming Language: Python
On line Tutorial
Download

• Source code (Linux, BSD (Mac) 
• Windows Executable 
• Tutorial
• TreeDyn

Version	Date	Homepage
02	22/May/2007

  THEA

Analyses of DNA chip data with ontologies

author: Claude Pasquier (in charge), Fabrice Girardot, Karim Jevardat de Fombelle, Richard Christen
License: GNU General Public License (GPL)
Natural Language: English
Operating System: OS independent
Programming Language: Java



Version	Date	Homepage
1.0	February 10, 2003

 Blast2Tree

Blast server for the identification of procaryotes

author: Olivier Croce
Natural Language: English
Operating System: OS independent
Programming Language: CGI/PHP/Ajax/HTML/JavaScript



-- Blast2Tree --

  Dashboard

e-Tool for data exchanges among partners, DNA chips design and developements

author: Olivier Croce
Natural Language: English
Operating System: OS independent
Programming Language: PHP/MySQL/HTML/JavaScript



Version	Date	Homepage
1.0	February 10, 2003

 Oligo Heat Map

Check thermodynamical parameters for PCR primers and compute graphical representation to show specificity of target sequences

author: Olivier Croce
Natural Language: English
Operating System: OS independent
Programming Language: PHP/JavaScript/HTML/

-- Access to OHM --     Help      OHM sources (.zip)     List of softwares for oligo design

  EmblEx

A cgi tool to parse and extract data from EMBL entries to various formats

author: Olivier Croce, Michael Lamarre
Natural Language: English
Operating System: OS independent
Programming Language: Perl/HTML/JavaScript

Online version is available here  (some options like ftp updates and BioSQL have been removed)



Version	Date	Download	Help
1.0	September 10, 2005	( ~400Mo )

Miscellaneous softwares

• Jane plugin
  Add a small panel to Jane server to retrieve PMID of publications
  - Jane server: http://www.biosemantics.org/jane/
  - Plugin for Jane (Firefox or Opera browsers only)
  Firefox: first, install Greasemonkey module (Tools-> Add modules -> search and install "GreaseMonkey"), then click on link below (Plugin for Jane), this will propose you to install the Jane plugin.
  Opera: download the plugin for Jane (right click on link, save target, save .js file somewhere on your hard-drive), go to Jane webpage (http://www.biosemantics.org/jane/), right click -> edit site preferences -> scripting -> select the path to the .js file, click ok. Reload the page to see the panel.
  
  
• EtBlast plugin
  Add a small panel to EtBlast server to retrieve PMID of publications
  - EtBlast server: EtBlast
  - Plugin for EtBlast (Firefox or Opera browsers only)
  Firefox: first, install Greasemonkey module (Tools-> Add modules -> search and install "GreaseMonkey"), then click on link below (Plugin for EtBlast), this will propose you to install the EtBlast plugin.
  Opera: download the plugin for EtBlast (right click on link, save target, save .js file somewhere on your hard-drive), go to EtBlast webpage (http://invention.swmed.edu/etblast/etblast.shtml), right click -> edit site preferences -> scripting -> select the path to the .js file, click ok. Reload the page to see the panel.
  
  
• Oligo Builder
  Get the oligomers from a set of target sequences by avoiding non-target sequences
  Oligo Builder

  SeqAm: "des sequences aux amorces" ("from sequences to probes")

Design of probes and reporters. Automatic + manual adjustments. Highly flexible

author: Sebastien Flavier
License: GNU General Public License (GPL)
Natural Language: English
Operating System: OS independent
Programming Language: Java



Version	Date	Homepage
1.0	February 10, 2003

  Programmes d'alignements multiples.

Les programmes d'alignement de séquences nucléiques

Tableau récapitulatif

Evaluations

Hosting of Alain Guenoche best products

ClassDense & BigClassDense: Use a distance matrix to make classes

author: Alain Guénoche
License: GNU General Public License (GPL)
Natural Language: French
Operating System: OS independent, command line
Programming Language: C



Package	Version	Date	Download
BigClassDense	1.0	2003
ClassDens	1.0	2003
BigClassDense.exe (windows)	1.0	2004
ClassDens.exe (windows)	1.0	2004
BigClassDenseOC (iterates on cutoff levels)	1.0	2004
BigClassDenseOC.exe (windows)	1.0	2004
python to run BigClassDenseO	1.0	2004

SubDiam: "The best divisive classification program"

author: Alain Guénoche
License: GNU General Public License (GPL)
Natural Language: French
Operating System: OS independent, command line
Programming Language: C



Package	Version	Date	Notes	Download
SubDiam	1.0	20043

Qualitree: "Compares how a newick tree represents truly a data matrix"

author: Alain Guénoche
License: GNU General Public License (GPL)
Natural Language: French
Operating System: OS independent, command line
Programming Language: C



Package	Version	Date	Notes	Download
Qualitree	1.0	2004