aliFreeFold & aliFreeFoldMulti
A program to predict the conserved secondary structures of homologous ribonucleic acid (RNA) sequences using an alignment-free approach.

DoubleRecViz
A program for visualizing and editing double reconciliations between phylogenetic trees at three levels: transcript, gene and species.

FsePSA
A program to compute pairwise alignments between coding DNA sequences while accounting for the length of frameshift translations.

ProCARs
A program to reconstruct Ancestral gene orders as CARs (Contiguous Ancestral Regions) with a progressive homology-based method.

Protein2GeneTree
A program to compute a genetree minimizing the sum of reconciliation costs with a protein tree and a species tree.

RNAFamViz
A tool for visualizing the evolution of RNA secondary structure motifs in a RNA family.

SpliceFamViz
A program to compute and visualize the multiple spliced alignments of transcript and gene sequences from a gene family.

SpliceAlnViz
An interactive visualization tool for multiple spliced alignment of genes and alternative transcripts of a gene family.

SpliceFamAlign & SpliceFamAlignMulti
A tool for computing the alignment of a spliced CDS against a gene sequence while accounting for the splicing structures of the input sequences, and then the inference of transcript splicing orthology groups in a gene family based on spliced alignments.

SuperProteinTree
A tool that computes a super protein tree given a set of protein clusters. It also reconstructs a gene tree using the double reconciliation with a protein tree and a species tree.

SimSpliceEvol
A new method for simulating the evolution of sets of alternative transcripts along the branches of an input gene tree.