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toolbar is an exact discrete optimization tool for graphical models. For most use cases, it has been obsoleted by toulbar2 (on GitHub).

This a the private clone archive of toulbar2. The real project is on GitHub. This one contains the "diverse solution" branch that needs to be pulled in the main repo (master)

A library of Cost Function Networks and other graphical model instances (MRF, PWMaxSat,...).

mechanistic-statistical environement

https://olivier.bonnefon.pages.mia.inra.fr/mse/

R'MES is a tool for studying word frequencies in biological sequences.

simulateur de l'invasion du moustique Aedes

X!TandemPipeline is a free software (GPL v3) that helps you to filter and group your peptide/protein identifications from MS/MS mass spectra.

Publication: J. Proteome Res. 2017, 16, 2, 494–503 -- https://doi.org/10.102

code de couplage 2d/1d sur le paysage SELOMMES

A suite of C++ programs developed for transposable element search and their annotation in large eukaryotic genome sequence. A part of the REPET package.

Multiple is a program for de novo discovery of DNA motifs corresponding to Transcription Factor binding sites based on a probabilistic model of the DNA sequence that incorporates expression data as covariates.

PAPPSOms++ is a comprehensive C++ library including useful functions to handle mass spectrometric data, either in a proteomics setting or for data visualization. Abstractions include peptides, proteins, isotopic clusters, mass/drift spectra...

Lightweight C++ and Java library to produce Open Document Spreadsheet (.ods) files. The main goal is to write data as simply as writing it to a simple text file (csv or tsv). Libodsstream allows yout to read and write ODS files as stream

set of usefull mass spectrometry and proteomics utilities used by the PAPPSO team (http://pappso.inra.fr/). Get ion tables from peptides, SVG drawings of MS/MS annotated spectrum, expected intensity ratio of isotopes from a peptide....

MassChroQ (Mass Chromatogram Quantification) is a powerful and versatile software that performs retention time alignment, XIC extraction, peak detection and quantification on data obtained from liquid chromatography-mass spectrometry techniques.

A clone of the PMRF code (MIT licence) to be able to add some minor bells and whistles for symmetry handling

PAPPSOms++ is a comprehensive C++ library including usefull functions to handle proteomics data (spectrum, peptides, ions, isotopes).

massXpert (of the http://www.msxpertsuite.org software collection) is a program that allows one to define brand new polymer chemistry definitions, to use them to define polymer sequences and to perform a large array of chemical simulations on them.