You can run these programs online

Phylogenetics

• AquaPony B. Cazaux, G. Castel, E. Rivals.
  Visualization and interpretation of phylogeographic information on phylogenetic trees
• CompPhy Fiorini N., Lefort V., Chevenet F., Berry V. and Arigon Chifolleau A-M.
  A web-based collaborative platform for comparing phylogenies
• EvoLaps Chevenet F., Fargette D., Bastide P., Vitré T, Guindon S.
  Advanced phylogeographic visualization
• FastME Desper R., Gascuel O.
  Distance based phylogeny reconstruction algorithm
• Phylogeny.fr
  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
• ReplacementMatrix Cuong Cao Dang, Vincent Lefort, Vinh Sy Le, Quang Si Le, and Olivier Gascuel.
  Maximum likelihood estimation of amino acid replacement rate matrix
• Scriptree François Chevenet, Olivier Croce, Maxime Hebrard, Richard Christen and Vincent Berry.
  Scripting phylogenetic graphics
• SMS Vincent Lefort, Jean-Emmanuel Longueville, Olivier Gascuel.
  Smart Model Selection in PhyML

NGS

• Motif David Martin, Vincent Maillol, Eric Rivals
  Fast and accurate genome-scale identification of DNA-binding sites
• MPscan Rivals E., Kalsi P., Salmela L., Kiiskinen P., Tarhio J.
  Fast localisation of multiple reads in genomes

Analysis of gene expression

• RED2 Mathieu Lajoie, Olivier Gascuel, Vincent Lefort, Laurent Bréhélin.
  Regulatory Element Discovery from Raw Expression Data

Sequences analysis

• MS ALIGN Berard S. and Rivals E.
  Pairwise ALIGNments of Mini Satellite maps
• STAR Rivals E. and Delgrange O.
  Algorithm to Search for Tandem Approximate Repeats