The Software

 Sequence analysis

• pLocalScore, Computing Local Score p-value.
  This program allows to compute asymptotic (Gumble's approximations) and exact p-value for the Local Score of one sequence.
• R'HOM, Research of HOMogeneous regions in DNA sequences.
  Hidden Markov Models for DNA sequences estimated by likelihood maximisation.
• R'MES, Finding Exceptional Motifs in Sequences
  A tool to evaluate the statistical significance of motif frequencies in biological sequences.
• SHOW, Structured HOMogeneities Watcher.
  Hidden Marlov Models for DNA sequences.
• SIC, Search Inverse Complementary.
  A tool to detect short inverted segments in a biological sequence.
• SPatt, Statistics for Patterns.
  A complete software package dedicated to the computation of pattern statistics on Markov chains.

 MicroArrays

• Anapuce,
  Functions for normalisation and differential analysis of microarray data
• VarMixt,
  Differential analysis of microarray data whose variances are modelled by a mixture model.
• kerfdr,
  A semi-parametric kernel-based approach to local FDR estimations

Association studies

• exact.allelic.test, A Fast Unbiased and Exact Allelic Test.
  An algorithm dedicated to case-control association studies using bi-allelic markers and allowing to compute fast unbiased exact p-values.

• LHiSA, Local High-scoring Segments for Association Studies.
  An algorithm dedicated to large-scale association studies which aims to identify segments of genome involved in a disease using local score.

 Networks

• Mix[Net/eR], Erdos-Rényi Mixture for Networks.
  A new probabilistic model for random graphs.

Physical mapping

• ISLAND
  Program to simulate the progress of an STS physical mapping project.