mreps : A package for finding tandem repeats in DNA sequences. Reference publication.
Software
I have been involved, to varying degrees, in the development of a range of bioinformatics and string-algorithms software. The following software is currently maintained:
YASS : Local alignment of DNA/RNA sequences, building dotpots. Reference publication. Wikipedia page. Maintained by Laurent Noé
ProPhyle : Phylogeny-based metagenomic classification of whole genome sequencing data. Maintained by Karel Břinda
Norine : A platform for non-ribosomal peptides. Maintained by Bonsai bioinformatics
The following are pieces of experimental software from different times, mostly not maintainted but potentially still of interest:
km-peeler : Implementation of Invertible Bloom Lookup Tables for k-mers. Reference publication
RNFtools : A naming format for simulated NGS reads and associated toolbox. Reference publication
path : Pairwise protein sequence alignment based on back-translation. Reference publication
StoRM : Mapping Illumina or SOLiD reads to a reference genome. Reference publication
ReBLOSUM : Rectangular BLOSUM matrices for protein comparison. Reference publication
grappe : Matching a subclass of regular expressions with wildcards. Reference publication
Designer : A C++ program for constructing combinatorial 2-designs.