Les plus fiers représentants des outils bioinformatiques à l'UQAM sont :

• Armadillo: plateforme de flux de travaux pour l'analyse phylogénétique et bioinformatique
• T-Rex: plateforme web pour l'analyse phylogénétique (versions Mac et Windows)
• Picante: R tools for integrating phylogenies and ecology
• HTS Corrector
• OVW: Optimal Variable Weighting
• Linear and Polynomial RDA and CCA
• Robinson and Foulds topological distance
• MiRdup: prediction et validation des microARN
• WMP: Wheat MicroRNA Portal
• PGR: Protein Graph Repository
• CaRNAval
  Organized collection of RNA Recurrent Interaction Networks (RIN), can annotate any structure file.
• RNAmigos
  Predict a small molecule binding profile (molecular fingerprint) given an RNA base-pairing pattern.
• BayesPairing
  Automatic identification of 3D structural modules in RNA sequences.
• RNA-MoIP
  Prediction of local 3D motifs from RNA secondary structure predictions.
• aRNhAck
  Prediction of RNA-binding interfaces using SHAPE data and MSA.
• IncaRNAtion
  Design of RNA sequences folding into target secondary structures with nucleotide distribution.
• achARNement
  Reconstruction of ancestral RNA sequences under multiple structural constraints.
• RNApyro
  Error-correction of RNA sequencing data using secondary structure information.
• IncaRNAfbinv
  Fragment-based design of RNA sequences.