You can run these programs online

• e-LEA3D
  A computational-aided drug design web server
• ESTTik
  A semi-automatic DNA sequence analysis and annotation pipeline for cDNA generation
• FastME Desper R., Gascuel O.
  Distance based phylogeny reconstruction algorithm
• HELIQUEST
  A web server to screen sequences with specific alpha-helical properties
• GMOTIS
  GMO Tracking Information System (in french)
• MPscan Rivals E., Kalsi P., Salmela L., Kiiskinen P., Tarhio J.
  Fast localisation of multiple reads in genomes
• MS ALIGN Berard S. and Rivals E.
  Pairwise ALIGNments of Mini Satellite maps
• Phylogeny pipeline
  Dedicated to reconstructing and analysing phylogenetic relationships between molecular sequences
• PhyloType Chevenet F., Jung M., Peeters M., de Oliveira T., Gascuel O.
  Searching for Virus Phylotypes
• PhyML Guindon S. and Gascuel O.
  Phylogenetic Maximum Likelihood
• PhySIC_IST Scornavacca C., Berry V., Lefort V., Douzery E.J.P., Ranwez V.
  Cleaning source trees to infer more informative supertrees (a recent development of the PhySIC method)
• PhySIC Ranwez V., Berry V., Criscuolo A., Fabre P.H., Guillemot S., Scornavacca C., Douzery E.J.P.
  Phylogenetic inference of Supetrees with Induction and non-Contradiction
• RED2 Mathieu Lajoie, Olivier Gascuel, Vincent Lefort, Laurent Bréhélin.
  Regulatory Element Discovery from Raw Expression Data
• ReplacementMatrix Cuong Cao Dang, Vincent Lefort, Vinh Sy Le, Quang Si Le, and Olivier Gascuel.
  Maximum likelihood estimation of amino acid replacement rate matrix
• SAT, SSR Analysis Tool
  A pipeline conceived to analyse sequences obtained from SSR (Simple Sequence Repeat) enriched libraries
• Scriptree François Chevenet, Olivier Croce, Maxime Hebrard, Richard Christen and Vincent Berry.
  Scripting phylogenetic graphics
• STAR Rivals E. and Delgrange O.
  Algorithm to Search for Tandem Approximate Repeats