Genomepop is flexible software that allows the forward simulation of DNA sequences in a metapopulation context under a variety of conditions. Users can input their own sequences or tell the program to generate them. Retro and recurrent mutation can be allowed or neglected. A number of populations with any migration model can be defined. Each population consists of a number N of sequences or genomes.
TSSV (Targeted characterisation of Short Structural Variation) is a program that does targeted characterisation of short structural variation. It can be used for STR analysis, or any other type of targeted analysis. It characterises any variation between a set of user-defined markers.
MaxSSmap is a GPU program with the aim of achieving comparable accuracy to Smith-Waterman but with faster runtimes. MaxSSmap identifies a local region of the genome followed by exact alignment.
CHROnicle is a package dedicated to the reconstruction of the complete evolutionary history of genomes. It is based on the analysis of the marks accumulated over evolutionary time left in the genomes by chromosomal rearrangements. CHROnicle is composed of four different programs: SynChro, PhyChro, ReChro and AnChro.
Fermi is a de novo assembler for Illumina reads from whole-genome short-gun sequencing. It also provides tools for error correction, sequence-to-read alignment and comparison between read sets. It uses the FMD-index, a novel compressed data structure, as the key data representation.