CRAC is a tool for analysing high-throughput sequencing reads against a reference genome. It was designed for RNA-seq and genomic reads, with predictions including variants, indels, splice junctions and chimeric RNAs.

Reference: CRAC: an integrated approach to the analysis of RNA-seq reads, Genome Biology 2013. DOI: 10.1186/gb-2013-14-3-r30.

Gk-arrays is a memory-efficient data structure for querying very large read collections, supporting fast exact searches in sequencing datasets.

Reference: Querying large read collections in main memory: a versatile data structure, BMC Bioinformatics 2011. DOI: 10.1186/1471-2105-12-242.

MPscan searches millions of reads or patterns in a genome without indexing the genomic sequence, using an efficient filtration strategy.

Reference: MPscan: Fast Localisation of Multiple Reads in Genomes, WABI 2009. DOI: 10.1007/978-3-642-04241-6_21.

QOD is a genome comparison method based on segmentation by similarity, designed as an alternative to multiple genome alignment for comparing related genomes.

Reference: An Alternative Approach to Multiple Genome Comparison, Nucleic Acids Research 2011. DOI: 10.1093/nar/gkr177.

RNA-Ribo Explorer is an interactive tool for mining and visualising ribosome profiling data, especially transcript-level translation signals.

Reference: RNA-Ribo Explorer: interactive mining and visualisation of Ribosome profiling data, bioRxiv 2021. DOI: 10.1101/2021.03.23.436679.

SAVAGE is a de novo assembler for viral quasispecies. It reconstructs viral haplotypes from sequencing reads using overlap graphs.

Reference: De novo assembly of viral quasispecies using overlap graphs, Genome Research 2017. DOI: 10.1101/gr.215038.116.

MS_ALIGN compares minisatellite maps under evolutionary models including insertion, deletion, mutation, tandem duplication and tandem deletion events.

References: Comparison of Minisatellites, Journal of Computational Biology 2003. DOI: 10.1089/10665270360688066; A Fast and Specific Alignment Method for Minisatellite Maps, Evolutionary Bioinformatics 2006. DOI: 10.1177/117693430600200025.

STAR searches for tandem approximate repeats in biological sequences, allowing approximate copies rather than only exact repeat units.

Reference: STAR: an algorithm to Search for Tandem Approximate Repeats, Bioinformatics 2004. DOI: 10.1093/bioinformatics/bth335.

DTscore reconstructs tandem duplication trees from distances between repeated copies, under a tandem duplication model.

Reference: An efficient and accurate distance based algorithm to reconstruct tandem duplication trees, Bioinformatics 2002. DOI: 10.1093/bioinformatics/18.suppl_2.S92.

PermuMatrix is a graphical environment for clustering and seriation analysis, especially for arranging gene expression profiles in optimal linear order.

Reference: PermutMatrix: a graphical environment to arrange gene expression profiles in optimal linear order, Bioinformatics 2005. DOI: 10.1093/bioinformatics/bti141.

RED2 discovers regulatory motifs from expression data without requiring a preliminary clustering step, by estimating motif densities in a continuous expression space.

Reference: Computational discovery of regulatory elements in a continuous expression space, Genome Biology 2012. DOI: 10.1186/gb-2012-13-11-r109.

BioNJ is an improved version of the Neighbor-Joining algorithm for distance-based phylogenetic reconstruction.

Reference: BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data, Molecular Biology and Evolution 1997. DOI: 10.1093/oxfordjournals.molbev.a025808.

PhyD* implements fast NJ-like algorithms, including NJ*, BioNJ* and MVR*, for reconstructing phylogenetic trees from incomplete distance matrices.

Reference: Fast NJ-like algorithms to deal with incomplete distance matrices, BMC Bioinformatics 2008. DOI: 10.1186/1471-2105-9-166.

IPK computes phylo-k-mers for a fixed phylogeny, producing databases that can be used for phylogenetic placement and metabarcoding workflows.

References: Computing Phylo-k-Mers, IEEE/ACM TCBB 2023. DOI: 10.1109/TCBB.2023.3278049; EPIK: Precise and scalable evolutionary placement with informative k-mers, Bioinformatics 2023. DOI: 10.1093/bioinformatics/btad692.

LSD estimates dated phylogenies using least-squares criteria, providing a fast method for molecular dating from branch lengths and temporal constraints.

Reference: Fast Dating Using Least-Squares Criteria and Algorithms, Systematic Biology 2016. DOI: 10.1093/sysbio/syv068.

EvoLaps grouped several phylogenetic models for protein evolution, including LG, LG4X, CAT/profile mixture models, mixture models for proteins and structure-aware models.

References: LG4X, DOI: 10.1093/molbev/mss112; LG, DOI: 10.1093/molbev/msn067; CAT, DOI: 10.1093/bioinformatics/btn445; protein mixture models, DOI: 10.1098/rstb.2008.0180; structure-based models, DOI: 10.1093/sysbio/syq002.

MLS amalgamates source trees defined at different taxonomic levels, allowing supertree construction when input trees do not share the same level of taxonomic resolution.

Reference: Amalgamating Source Trees with Different Taxonomic Levels, Systematic Biology 2013. DOI: 10.1093/sysbio/sys090.

Mowgli reconciles gene/species or host/parasite trees under parsimony, accounting for speciations, duplications, transfers, losses and ecological constraints. MowgliNNI extends this framework by exploring local rearrangements around weakly supported gene-tree edges.

References: reconciliation algorithm, DOI: 10.1007/978-3-642-16181-0_9; ecological constraints, DOI: 10.1111/1755-0998.12897; gene-tree uncertainty, DOI: 10.1007/978-3-642-33122-0_10; MowgliNNI, DOI: 10.1186/1748-7188-8-12.

PhyloType searches for virus phylotypes, i.e. groups of taxa sharing both a phylogenetic history and common trait values.

Reference: Searching for virus phylotypes, Bioinformatics 2013. DOI: 10.1093/bioinformatics/btt010.

Site officiel : http://phylotype.org/

PhySIC is a veto supertree method based on non-contradiction and induction principles. PhySIC_IST extends this approach by cleaning source trees to infer more informative supertrees.

References: PhySIC, DOI: 10.1080/10635150701639754; PhySIC_IST, DOI: 10.1186/1471-2105-9-413.

RAPPAS performs rapid alignment-free phylogenetic placement of metagenomic sequences using ancestral-sequence-derived k-mers.

Reference: Rapid alignment-free phylogenetic identification of metagenomic sequences, Bioinformatics 2019. DOI: 10.1093/bioinformatics/btz068.

ReplacementMatrix estimates amino-acid replacement rate matrices by maximum likelihood from protein alignments.

Reference: ReplacementMatrix: a web server for maximum-likelihood estimation of amino acid replacement rate matrices, Bioinformatics 2011. DOI: 10.1093/bioinformatics/btr435.

ScripTree is a scripting tool for producing and annotating phylogenetic graphics, usable as a standalone program or inside automated pipelines.

Reference: ScripTree: scripting phylogenetic graphics, Bioinformatics 2010. DOI: 10.1093/bioinformatics/btq086.

SDM is a fast distance-based approach for building trees and supertrees in phylogenomics.

Reference: SDM: a fast distance-based approach for (super)tree building in phylogenomics, Systematic Biology 2006. DOI: 10.1080/10635150600969872.

SSIMUL extracts speciation signal from multi-copy gene families, helping build species trees from larger portions of phylogenomic databases.

Reference: Building species trees from larger parts of phylogenomic databases, Information and Computation 2011. DOI: 10.1016/j.ic.2010.11.022.

TreeDyn is a tree visualization and annotation tool designed for interactive graphical analysis of phylogenetic trees.

Reference: TreeDyn: towards dynamic graphics and annotations for analyses of trees, BMC Bioinformatics 2006. DOI: 10.1186/1471-2105-7-439.

SylvX is a viewer for phylogenetic tree reconciliations, with tools for displaying, comparing and annotating reconciled trees.

Reference: SylvX: a viewer for phylogenetic tree reconciliations, Bioinformatics 2016. DOI: 10.1093/bioinformatics/btv625.