CLASS2 Fast and accurate transcript assembly of RNA-seq reads aligned to a reference genome. 
CLASS An alternative splicing-aware genome-guided transcript assembler for RNA-seq reads.
JULiP Distributed software for intron selection by simultaneous analysis of many RNA-seq samples.
ASprofile A package for discovery, quantification and comparison of alternative splicing events in and across multiple samples.
Rascaf An efficient algorithm that leverages the contiguity information in RNA-seq reads to improve a genome assembly.
Lighter Fast and efficient error correction without counting for Illumina DNA-seq reads, using a Bloom filter.
Rcorrector Fast and efficient error correction of Illumina RNA-seq reads using read-level and k-mer-level read count thresholds.
rddChecker A tool for detecting RNA-DNA differences in RNA-seq data potentially created by RNA editing.
  Gene Finding and Genome Analysis
gencomp Software for comparing two sets of gene annotations.
sim4 Software for aligning a cDNA (EST, mRNA) and one or several genomic sequences, alowing for introns.
sim4cc A tool for cross-species spliced alignment of one cDNA and one or several genomic sequences.
sim4db A fast and scalable suite of utilities for spliced alignment of collections of EST and mRNA sequences to genomic sequences.
leaff A library for fast and scalable manipulation of fasta sequence databases.
ESTmapper Software for high-throughput spliced alignment of millions of cDNA sequences to a reference genome.
ATAC An accurate program for aligning whole genomes.
AIR An automated pipeline for gene and alternative splicing annotation from EST and cDNA spliced alignments to a genome, based on the splice graph.
  Host-Pathogen Genomics
Enterix    Web servers for visualization of pairiwise and multiple alignments and annotations of bacterial and viral genomes.