You can download these software

• WAVES Chakiachvili M., Milanesi S., Arigon Chifolleau A.-M., Lefort V.
  A Web Application for Versatile Enhanced bioinformatic Services

Phylogenetics

• BIONJ Gascuel O.
  Improved version of NJ, based on a model of sequence data
• EPIK Romashchenko N., Linard B., Pardi F, Rivals E..
  Precise and scalable evolutionary placement with informative k-mers
• FastME Desper R., Gascuel O.
  Distance based phylogeny reconstruction algorithm
• IPK Romashchenko N., Linard B., Rivals E., Pardi F.
  Inference of Phylo-K-mers
• LSD To T.-H., Jung M., Lycett S. and Gascuel O.
  Fast dating software using least-squares criteria
• New phylogenetic models for the evolution of proteins Quang L.S., Gascuel O., Lartillot N.
• PhyML Guindon S., Gascuel O.
  Phylogenetic Maximum Likelihood
• MLS Berry V., Bininda-Emonds O.R.P, Semple C.
  Amalgamating Source Trees with Different Taxonomic Levels
• Mowgli and MowgliNNI Doyon J-P., Nguyen T-H.
  Fast reconciliation of gene and species tree accounting for gene transfers, duplications and losses, as well as gene tree uncertainty
• PEWO Linard B., Romashchenko N., Pardi F., Rivals E.
  Placement Evaluation WOrkflows
• PhyD* Criscuolo A., Gascuel O.
  Fast NJ-like algorithms to deal with incomplete distance matrices
• 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 Supertrees with Induction and non-Contradiction
• RAPPAS Linard B., Swenson K., Pardi F.
  Rapid, Alignment-free, Phylogenetic Placement via Ancestral Sequences
• SDM Criscuolo A., Berry V., Douzery E.J.P., Gascuel O.
  Fast Distance-based Approach for (Super)Tree Building in Phylogenomics
• SSIMUL Scornavacca C., Berry V., and Ranwez V.
  Speciation SIgnal extraction from MULtigene families
• TreeDyn Chevenet F., Brun C., Banuls A.L., Jacq B., Christen R.
  Towards dynamic graphics and annotations for analyses of trees

NGS

• CRAC Philippe N. , Salson M. , Commes T. and Rivals E.
  An integrated approach to the analysis of RNA-seq reads
• Gk-arrays Philippe N., Salson M., Lecroq T., Leonard M., Commes T., Rivals E.
  Structure to index NGS reads
• LoRDEC Salmela L. and Rivals E.
  A hybrid error correction program for long, PacBio reads
• LoRMA Salmela L., Walve R., Rivals E., Ukkonen E.
  A self correction program for long reads (PacBio, Nanopore)
• MPscan Rivals E., Kalsi P., Salmela L., Kiiskinen P., Tarhio J.
  Index free mapping of multiple short reads on a genome
• MS_Align Bérard S., Rivals E.
  Comparison of minisatellites
• PEWO Linard B., Romashchenko N., Pardi F., Rivals E.
  Placement Evaluation WOrkflows
• QOD Mancheron A., Uricaru R., Rivals E.
  An Alternative Approach to Multiple Genome Comparison
• RRE Paulet D., David A., Rivals E.
  RNA-Ribo Explorer: interactive mining and visualisation of Ribosome profiling data
• RSCU Paulet D., David A., Rivals E.
  Ribo-seq enlightens Codon Usage Bias
• SAVAGE Baaijens J., Zine El Aabidine A., E. Rivals, and Schoenhuth A.
  A de novo assembler for viral quasispecies
• STAR Delgrange O., Rivals E.
  Algorithm to Search for Tandem Approximate Repeats

No longer actively maintained

• DTscore Elemento O., Gascuel O.
  Distance based algorithm to reconstruct the duplication history of tandemly repeated sequences
• PermutMatrix Caraux G., Pinloche S.
  Graphical software for analyzing and visualizing gene expression data