Software for bioinformatics

Original computer tools (softwares, programs, scripts, prototypes or programming libraries) resulting from (and developed during) my research projects (not necessarily by me)
If you find these softwares useful, please cite the corresponding articles. See the complete references in my Publication List.

Computer programs for processing Next Generation Sequencing data

RNA-Ribo-Explorer (RRE): interactive, multi-platform software to explore jointly RNA-seq and Ribo-seq data sets.
Download: https://gite.lirmm.fr/rivals/RRE
Preprint: Paulet et al. BioRXiv doi:10.1101/2021.03.23.436679, March 2021.
SHERPAS: Rapid screening and detection of inter-type viral recombinants using phylo-k-mers
Download: https://github.com/phylo42/sherpas
Publication: Scholz et al. Bioinformatics, btaa1020, 17 Dec. 2020.
PEWO: a collection of workflows to benchmark phylogenetic placement
Download: https://github.com/phylo42/PEWO/wiki
Publication: Linard et al. Bioinformatics, btaa657, 22 July 2020.
SAVAGE: a de novo assembler for viral quasispecies
Download: https://bitbucket.org/jbaaijens/savage
Publication: Baaijens et al. Genome Research 27: 835-848, 2017.
RSCU_RS: a R program for assessing synonymous codon usage bias from Ribo-sequencing data.
Download: http://www.lirmm.fr/~rivals/rscu/ ;
Publication : Paulet et al. DNA Research dsw062. doi: 10.1093/dnares/dsw062, 2017.
LoRMA: a self correction program for long reads (PacBio, Nanopore)
Download: https://gite.lirmm.fr/lorma/lorma-releases/wikis/home
Publication: Salmela et al Bioinformatics 33(6): 799-806, doi:10.1093/bioinformatics/btw321, 2017.
LoRDEC: a hybrid, accurate and efficient tool for long read error correction.
Download http://atgc.lirmm.fr/lordec/ ;
Publication: Salmela & Rivals Bioinformatics 2014.
CRAC: An integrated approach to NGS read analysis.
Download http://www.atgc-montpellier.fr/crac/ ;
Publication: Philippe et al. Genome Biology 2013.
Gk-arrays: A C++ library for querying large read collections in main memory. It implements a versatile data structure.
Download http://www.atgc-montpellier.fr/gkarrays/ ;
Publication: Philippe et al. BMC Bioinformatics 2011.
MPscan: an index-free, exact mapping software for multiple short reads on a genome. Very useful for Digital Gene Expression (formerly SAGE) data.
Download or use on-line : http://www.atgc-montpellier.fr/mpscan/ ;
Publication: Rivals et al. WABI, LNCS, 2009.

Computer programs for sequence analyses and evolutionary analyses.

AQUAPONY: an interactive visualisation tool for phylogenies with ancestral annotations and trait evolution scenarios
Publication: HAL: https://hal-lirmm.ccsd.cnrs.fr/lirmm-01702654v1, feb. 2018
Motif: a web-service for searching binding sites in whole genomes
Publication: IEEE Int Conf. on Bioinformatics and Biomedicine (BIBM 2018) #29, 2018
YOC: A new strategy for pairwise alignment of collinear genomes
Download https://github.com/ruricaru/YOC ;
Publication : Uricaru et al. BMC Bioinformatics 2015.
QOD: An Alternative Approach to Multiple Genome Comparison. A new software for whole genome comparison at the DNA level and annotation transfer.
Download http://www.atgc-montpellier.fr/qod/ ;
Publication : Mancheron et al. Nucleic Acids Research 2011.
PPR: annotate simultaneously all protein motifs known to occur in the PentatricoPeptide Repeat protein family. Produce a single alignment with all motifs deltimited in it.
Access on-line.
STAR: Search for Tandem Approximate Repeats in a DNA sequence.
Access or download: http://www.atgc-montpellier.fr/star/ ;
Publication: Delgrange & Rivals, Bioinformatics 2004.
MS_Align: Pairwise alignment of minisatellite maps.
Download or use: http://www.atgc-montpellier.fr/ms_align/ ;
Publication: Bérard et al. J. Computational Biology 2003.
2ZIP: prediction of Leucine Zipper domain from the protein sequence.
Access on-line or download: http://www.lirmm.fr/2zip/
Publication: Bornberg, Rivals, Vingron Nucleic Acids Research 1997
GeneNest: gene indices for human, mouse, zebrafish and Arabidopsis thaliana. Browse them with a nice interface.
Access: http://genenest.molgen.mpg.de/ (not maintained anymore);
Publication: Haas et al. Trends in Genetics 2000.
Transformation Distance: pairwise compare sequences and reveal segment inversions, duplications.
Download: http://www.lifl.fr/~varre/TD/td.html;
Publication: Varré et al. Bioinformatics 1999
SearchRepeats: detection of exact repeats by a compression algorithm.
Soft unavailable nowadays ;-).
Publication: Rivals et al. GIW 1997 ;
QUASAR: a fast sequence similarity search algorithm for multiple queries. (Broken link)
Soft unavailable nowadays ;-).
Publication: Burkhardt, Rivals et al. RECOMB, 1999;