Page in construction.
Most of the algorithms developed locally by members of BAMBOO are hosted at the Rhône-Alpes Bioinformatics Center (PRABI, "Pôle Rhône Alpin de BioInformatique"). A number of them are hosted by another institution in France or abroad to which an ex-student is now attached or from where came a more recent member of BAMBOO. Contributors to the paper but not to the code are not indicated in the table. See the paper(s) for this.
|Name||Main implementer||Brief description|
|MiGaL||Julien Allali||MiGaL is a software for comparing RNA secondary structures.|
|seq++||Vincent Miele with also Pierre-Yves Bourguignon, Sophie Lebre, David Robelin, Gregory Nuel, Hugues Richard (SSB)||Seq++ modularity enables the study of genomic data at abstract levels, as well as any biological process which can be seen as a succession of states taken in a finite ensemble.|
|BaobabLUNA||Marília D. V. Braga||This software is a package dedicated to sorting permutations and signed permutations by reversals.|
It implements: 1. an algorithm to sort a signed permutation by reversals, and 2. an algorithm to enumerate one solution per trace of sorting by reversals.
|Ed’Nimbus||Pierre Peterlongo||Ed’Nimbus is a software for filtering DNA sequences prior to finding long approximate repetitions.|
|MotusWeb||Vincent Lacroix with contributions from Odile Rogier, Ludovic Cottret, Fabien Jourdan||Coloured motif search and inference in vertex coloured graphs such as metabolic networks and interaction networks (see also non web version for more features).|
|Sarment||Laurent Guéguen||Sarment is a source package, under GPL License, of object-oriented Python modules for sequence segmentation via HMM analysis and Maximal Predictive Partitioning.|
|Alfacinha||Leonor Palmeira, Laurent Guéguen||Alfacinha is a source-package of object-oriented Python modules for sequence evolution allowing for neighbor-dependent substitutions. The package is aimed at simulating the evolution of sequences along phylogenetic trees.|
|MareyMap||Clément Rezvoy, Laurent Guéguen, Gabriel Marais||MareyMap is a meiotic recombination rate estimation program.|
|MixNet||Vincent Miele, Franck Picard, with also Christophe Ambroise, Jean-Jacques Daudin, Hugo Zanghi, Stéphane Robin (SSB)||MixNet is a software package based on a new probabilistic model for random graphs called MixNet (Erdös-Renyi Mixture for Networks). This model is based on the hypothesis that real networks are made of classes which show specific connectivity patterns.|
|Pepline||Alain Viari||Pepline is a fully automated software to map MS/MS fragmentation spectra of enzymatic digested peptides to genomic DNA sequences. The approach is based on Peptide Sequence Tags (PSTs) resulting from partial interpretation of the MS/MS spectra.|
|Tuiuiu||Pierre Peterlongo, Gustavo Sacomoto, Alair Pereira do Lago||Tuiuiu is a filter which removes from a sequence or a set of sequences regions as large as possible that are guaranteed not to contain certain well-defined types of repeats. Tuiuiu may be used as a preliminary step before applying a multiple local aligner.|