Banques et logiciels par ftp
English version
En général, après la connexion "ftp", listez par la commande "ls" ou "dir" et si vous n'avez pas l'information désirée, allez dans le répertoire pub.
Banques
- Sites principaux
- Sites spécialisés
Logiciels
- Catalogues
- Sites principaux
- EBI :
ftp.ebi.ac.uk (Unix, VMS, Mac, PC) Bio Catalog, copie à Pasteur
- EMBL :
ftp.embl-heidelberg.de (Unix, VMS, Mac, PC)
- Biology and Microbiology software 101science
- Indiana :
ftp.bio.indiana.edu (Mac, PC)
- IUBio (USA)
iubio.bio.indiana.edu, ou encore www
- Java-based Molecular Biology Work Bench EMBL
- NIG :
ftp.nig.ac.jp (Unix, VMS, Mac, PC)
- Open Molecule Foundation (Applets and Java packages for the bio- and chemo- informatics communities) ICSTM (UK)
- Pasteur (France) :
ftp.pasteur.fr
- Sites spécialisés ou hors archive
- 3DNA (package for analyzing and rebuilding 3-dimensional nucleic acid structures) Rutgers (USA)
- ABBESS (Approximation of the Basic Bayesian Evidence for Sequence Segmentation) BioSS (UK)
- Acana (an accurate anchoring alignment of divergent sequences) NIEH (USA)
- ACEDB, AcePerl ... CSHL, voir aussi acedb
- AClAP (autonomous hierarchical agglomerative cluster analysis based protocol to partition conformational datasets) Bologne (Italie)
- ACNUC Retrieval System PBIL (France)
- ACT (DNA sequence comparison viewer based on Artemis) Sanger (UK)
- ADE-4 (Exploratory and Euclidean methods in Environmental sciences) PBIL (France)
- ADP_EM (fast exhaustive multi-resolution docking for high-throughput coverage) Madrid (Espagne)
- AFold (analysis of internal loops within the RNA secondary structure in almost quadratic time) NCBI (USA)
- AGLAM (adding sequence context to a Markov background model improves the identification of regulatory elements) NCBI (USA)
- AiO (a program integrating Oligo ordering/Data Base and DNA/Protein programs) Dusseldorf (Allemagne)
- AIS (almost invariant sets) EBI (UK)
- AL2CO (Calculates Positional Conservation in a Protein Sequence Alignment) Texas (USA)
- ALES (cell lineage analysis and mapping of developmental events) DKFZ (Allemagne)
- ALGGEN (Algorithmics and Genetics : Dotlet) Barcelona (Espagne)
- ALIDOT (Detecting Conserved RNA Structures) Wien (Autriche)
- Alien_hunter (interpolated variable order motifs for identification of horizontally acquired DNA) Sanger (UK)
- Align-m (multiple alignment of highly divergent sequences) Bruxelles (Belgique)
- AlignACE Harvard (USA)
- Alignment Editors SeaView (France)
- ALOHOMORA (a tool for linkage analysis using 10K SNP array data) Berlin-Buch (Allemagne)
- AlphaSimp (Simplifying amino acid alphabets by means of a branch and bound algorithm and substitution matrices) CRIBI (Italie)
- ALSE (discovers the common patterns in a set of DNA sequences) Pokfulam (Hong Kong)
- AMAP (multiple alignment by sequence annealing) Berkeley (USA)
- AMBER (Assisted Model Building with Energy Refinement) SRI
- Amplicon (software package for designing PCR primers on aligned DNA sequences) Kingston (Australie)
- AMSOL (SCF Program for Free Energies of Solvation) UMN (USA)
- Analytical Biostatistics software (sequence analysis, ligand binding, gene expression) NIH (USA)
- Andrew Martin's page (Torsions, ProFit, QTree, MINT, Cluster)
- ANDY (a general, fault-tolerant tool for database searching on computer clusters) Berkeley (USA)
- ANeCA (automation of Nested Clade Phylogeographic Analysis) Reading (UK)
- Angler: A Browser of C.elegans Embryo Development In Time and Space Sanger (UK)
- ANTHEPROT (DOS, WINDOWS et IBM rs6000) PBIL (France)
- APAT (an extensible automated protein annotation tool: standardizing input and output using validated XML) Londres (UK)
- Apollo (Drosophila Genome Browser) BDGP
- ARB (A Software Environment for Sequence Data) Max-Planck, ou encore (Allemagne)
- ARCS (an aggregated related column scoring scheme for aligned sequences) Cleveland (USA)
- ARLEQUIN (population genetic data analysis) Geneva (Suisse)
- ARTEMIS (DNA sequence viewer and annotation tool) Sanger (UK)
- Molecular Assembly Sequence Software (Macintosh) Carol
- ASPEX Package (Affected Sib Pair Exclusion Mapping) Stanford (USA)
- ATGC, plateforme de bioinformatique du LIRMM Montpellier (France)
- ATR (exhaustive whole-genome tandem repeats search) Singapour
- AuberGene (a sensitive genome alignment tool) Amsterdam (The Netherlands)
- AutoDock (automatic docking of flexible ligands to macromolecules) SRI (USA)
- BACCardI (a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison) Bielefeld (Allemagne)
- BADASP (predicting functional specificity in protein families using ancestral sequences) Dublin (Irlande)
- BALLView (a tool for research and education in molecular modeling) Saarbrucken (Allemagne)
- BAli-Phy (simultaneous Bayesian inference of alignment and phylogeny) UCLA (USA)
- BAPS 2 (enhanced possibilities for the analysis of genetic population structure) Helsinki (Finlande)
- Barton group software (Alscript, Amas, Amps, JPred, OC, Stamp, Map, Scanps, 3Dee, ProEST, ..) Dundee (UK)
- Bass (Lane Tracking and Base Calling for Automated DNA Sequencers) MIT (USA)
- BIAS (Bioinformatics Integrated Application Software) Montreal (Canada)
- BIAS (a novel sensitive method for the detection of user-defined compositional bias in biological sequences) Albany (USA)
- BicAT (a graphical user interface software for the analysis of gene expression data) ETHZ (Suisse)
- Bio3d (an R package for the comparative analysis of protein structures) UCSD (USA)
- BioArray (a tool to analyze macroarray images) Hertfordshire (UK)
- BIOCHAM (an environment for modeling biological systems and formalizing experimental knowledge) INRIA (France)
- Bioconductor (open source for the analysis and comprehension of genomic data) bioconductor
- BIODEV (MatInd, ConsInspector, CoreSearch, GenomeInspector, FastM, Model generator, DIALIGN) BIODEV (Allemagne)
- BioDownloader (bioinformatics downloads and updates in a few clicks) Philadelphia (USA)
- BioEdit (user-friendly sequence alignment editor which runs on W95, W98, NT) North Carolina (USA)
- BioEditor (simplifying macromolecular structure annotation) SDSC (USA)
- Bioinformatics Lab (Euler, Grimm, MGR, MultiProfiler, Splicing graphs, Pattern Branching, Euler short read assembler) UCSD (USA)
- Bioinformatics Research Group (Arcade, CGHdist, Genoma map viewer, Gridmap, MPP, Plasmid drawing, RAT) JIC (UK)
- Bioinformatics software Bioinformatics
- Bioinformatics source SourceForge
- BioJava (open-source project) BioJava.org
- BioLinux packages
- Biological Data Representation and Query (QuickPDB, MMQL, MEME, etc..) SDSC (USA)
- Biological software developed at Pasteur Institute (France)
- BioMart (a simple, distributed data integration system with powerful query capabilities) EBI (UK)
- Biomer (Java-based on-line biomolecular modeling package) SRI (USA)
- BioMercator (integrating genetic maps and QTL towards discovery of candidate genes) INRA (France)
- BioNetBuilder (automatic integration of biological networks) New York (USA)
- Biopackages (currently provides packages as RPMs for Fedora Core Linux, CentOS Linux, and Apple Darwin) UCLA
- Bioperl Proposal for Perl5 Objects for Sequences, Alignments, and Phylogenies Georg Fuellen (VSNS : Allemagne), voir aussi BioPerl, voir aussi EBI (UK)
- Biophp (project and module code) Bioinformatics
- BioQuery (an object framework for building queries to biomedical databases) Oregon (USA)
- BioBrew (an open source Linux cluster distribution for bioinformatics) Bioinformatics
- BioShell (a package of tools for structural biology computations) Warsaw (Pologne)
- BioSVG (Perl framework to generate Scalable Vector Graphics) CCMB (Inde)
- BioTEX (LaTex2 bio extensions) Tuebingen (Allemagne)
- BioWidgets Consortium (Graphical displays of genome data) Berkeley (USA)
- BioWidgets for Java CBIL (USA)
- Biskit (a software platform for structural bioinformatics) Pasteur (France)
- BLAST et BLAST2.0.2 NCBI (USA)
- BLAST2 Wu-archives (USA)
- WebBLAST2 NHGRI (USA)
- BlastAlign (a program that uses blast to align problematic nucleotide sequences) Oxford (UK)
- BlastXtract (a new way of exploring translated searches) Cork (Irlande)
- Blast (longer words for protein seeding) NCBI (USA)
- Blixem (a graphical blast viewer) Karolinska (Suède)
- BMapBuilder (building chromosome-wide LD maps) Grenade (Espagne)
- BNetDyn (stochastic boolean network dynamics ) SIB (Suisse)
- BRAGI (protein modelling and display program) GBF (Allemagne)
- BTL (Bioinformatics Template Library) Birbeck (UK)
- Bystroff Lab Downloads (Masker, Hmmstr, Protean, Hmmsum) New-York (USA)
- C-Hunter (identifying clusters of functionally related genes in genomes) Texas (USA)
- caCORE (common infrastructure for cancer informatics : caBIO, caDSR, EVS) NCI (USA)
- CADLIVE (a grid layout algorithm for automatic drawing of biochemical networks) Fukuoka (Japon)
- caGrid (design and implementation of the core architecture of the cancer biomedical informatics grid) NIH (USA)
- Calign (aligning sequences with restricted affine gap penalties) Indiana (USA)
- CAP (Contig Assembly Program) CSD (USA)
- CAP (conformation angles package displaying the conformation angles of side chains in proteins) Bangalore (Inde)
- CAPS (coevolution analysis using protein sequences) Dublin (Irlande)
- CARNAC (Computer Alignment of RNA by Cofolding) LIFL (France)
- CarthaGene (multipopulation integrated genetic and radiation hybrid mapping) INRA (France)
- Case group (Amber, Nabs, Rnamotif, Shifts) SRI (USA)
- CBA (consistency based alignment (3D)) Stanford (USA)
- CBCB software (Glimmer, Twain, GlimmerHMM, TigrScan, JigSaw, GeneSplicer, Mumer, Amos, Minimus, Bambus, Elph, TransTerm, OperonDB ..) Maryland (USA)
- CBIL Tools (GenLang, BioWidgets, TESS, CPL) CBIL (USA)
- CBS Software CBS : Populus - Promoter Scan (Minnoseta)
- CCMS Software (Xtalview, Shape...) SDSC (USA)
- CCODE (Chimera and Cross-Over DEtection) Séville (Espagne)
- CCP13 Software (Conv, Corfunc, Fdscale, Fit, Fix, ..) Daresbury (UK)
- CD-HI / CD-HIT (for clustering large protein database at high sequence identity threshold) San Diego (USA), voir aussi bioinformatics
- Cellware (modeling and simulation tool for modeling cellular transactions) SBG-BI (Singapore)
- Cerebral (a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation) Vancouver (Canada)
- CFinder (locating cliques and overlapping modules in biological networks) Budapest (Hongrie)
- ChemWeb (to draw chemical structures) SoftShell (USA)
- Chime Resources Massachusetts (USA), voir aussi MDL
- ChromoScan (a scan statistic application for identifying chromosomal regions in genomic studies) Michigan (USA)
- Circles (comparative analysis of RNA secondary structure) Glasgow (UK)
- Cis-enrichment (tool to study the enrichment of Transctional Regulatroy Sites) Nanjing (Chine)
- CisPlusFinder (identifying cis-regulatory modules by combining comparative and compositional analysis of DNA) Cologne (Allemagne)
- CITA (programming interface that allows access to one or more ACEDB databases through CORBA) JIC (UK)
- Clann (investigating phylogenetic information through supertree analyses) Kildare (Irlande)
- ClassMaker (electrophoretic data classification for phylogenetics and biostatistics) Perugia (Italie)
- Clearcut (a fast implementation of relaxed neighbor joining) Moscou (Russie)
- Cleaver (software for identifying taxon specific restriction endonuclease recognition sites) Kingston (Australie)
- CLENCH (a program for calculating Cluster ENriCHment using the Gene Ontology) Stanford (USA)
- CloneIt: finding cloning strategies, in-frame deletions and frameshifts INRA (France)
- CLUSTAG (hierarchical clustering and graph methods for selecting tag SNPs) Hong Kong
- Clustal W and Clustal X version 2.0 EBI (UK)
- ClustalX (ClustalW avec interface graphique : Unix, NT, Macintosh) Strasbourg (France)
- cluster_boost (genomic sweeping for hypermethylated genes) Duke (USA)
- ClusterControl (a web interface for distributing and monitoring bioinformatics applications on a Linux cluster) Graz (Autriche)
- Clustering protein sequences (summarize and interpret your dendrogram) Taipei (Taiwan)
- Cn3D (a 3D molecular structure viewer and W3 helper (Entrez)) NCBI
- COBALT (constraint-based alignment tool for multiple protein sequences) NCBI (USA)
- Co-Bind, Landscape, GenParser, Consensus Washington (USA)
- ColorHOR (graphical algorithm for fast scan of alpha satellite higher-order repeats) Zagreb (Croatie)
- ComAlign (Combining many multiple alignments in one improved alignment) Aarhus (Danemark)
- ComBin (genetic software package developed for the construction of ultra-dense linkage maps) Wageningen (Netherlands)
- Combo (a whole genome comparative browser) MIT (USA)
- Comp3D (comparing gene expression networks in a multi-dimensional space to extract similarities and differences between organisms) ENS (France)
- COMPAM (visualization of combining pairwise alignments for multiple genomes) Indiana (USA)
- Compressed suffix tree-a basis for genome-scale sequence analysis Helsinki (Finlande)
- COMPUCELL (a multi-model framework for simulation of morphogenesis) Missouri (USA)
- Computational Biology Group - DAIMI (ComAlign, CombAt, HMMComp, Hudson, RecPars, StatAl, Qdist ...) Aarhus (Danemark)
- Computational Biology tools (Panorama, Primo, Pompous, Signal, SNPCEQer, Elxr ..) UTSMC (USA)
- Computational Tools (Molecular graphics and dynamics : BioCore, VMD , namd, HP cluster, MDTools) TBG (USA)
- CONSEL (for assessing the confidence of phylogenetic tree selection) Tokyo (Japon)
- ConStruct (prediction of conserved secondary structure of a set of homologous single-stranded RNA) Duesseldorf (Allemagne)
- COPASI (a COmplex PAthway SImulator) Blacksburg (USA)
- COPYCAT (cophylogenetic analysis tool) Tübingen (Allemagne)
- CORBA-Java based Application Wrapper EBI (UK)
- CpGProD (CpG Island Promoter Detection) PBIL (France)
- CRANN (detecting adaptive evolution in protein-coding DNA sequences) Maynooth (Irlande)
- CREx (inferring genomic rearrangements based on common intervals) Leipzig (Allemagne)
- CSPro (identification and visualization of cage-shaped proteins) Hangzhou (Chine)
- CS-PSeq-Gen (Simulation of protein sequences under constraints) Jussieu (France)
- CTree (analysis of clusters on phylogenetic trees) Manchester (UK)
- Cyclone (java-based querying and computing with Pathway/Genome databases) Evry (France)
- CyDAS (a cytogenetic data analysis system) Marburg (Allemagne)
- Cyto-Sim (a formal language model and stochastic simulator of membrane-enclosed biochemical processes) Catanzaro (Italie)
- DaliLite (pairwise structure comparison and database searching) EBI
- DAMBE (Data Analysis in Molecular Biology and Evolution) Ottawa (Canada)
- Darwin CBRG (Suisse)
- DASS (efficient discovery and p-value calculation of substructures in unordered data) Jena (Allemagne)
- Dating (comparative phylogenetic approach for dating whole genome duplication events) Georgia (USA)
- Debian-Med (Biologie moléculaire et génétique) debia-med
- DEODAS (DEgenerate Oligo Nucleotide Design & Analysis System) Sourceforge
- Dependency (to separate functional from phylogenetic correlations in protein alignments) Toronto (Canada)
- Detection and analysis of synaptic events in intracellular electrophysiological recordings Pasteur (France)
- Detecting high-order interactions of single nucleotide polymorphisms using genetic programming
- DGSplicer (prediction of splice sites with dependency graphs and their expanded bayesian networks) Hsinchu (Taiwan)
- DICOPROT (DICHROism of PROTeins) IBCP (France)
- Dizzy (a method for estimating stochastic noise in large genetic regulatory networks) Seattle (USA)
- DINO (Visualizing Structural Biology) Biozentrum (Suisse)
- DISCAS (characterization of chemical carcinogens studied by the cascade model) Nishinomiya (Japon)
- DIVCLUS (protein sequence domain clustering program) MRC (UK)
- DNArchitect (program designed to automate and simplify analysis of molecular biology sequences, similar to the program "DNA Strider") Savannah
- DNAdrawJ (program used to prepare DNA and protein sequence data for publication) dnadraw
- DNA hybridization partners in a sequence database Washington (USA)
- DnaSP, DNA Sequence Polymorphism Barcelone (Espagne)
- DOCK (Molecular docking simulations) UCSF (USA)
- Domain Finder (characterization of dynamical domains in proteins) Orléans (France)
- Dotter (a dot-matrix program with interactive greyscale rendering for genomic DNA and Protein sequence analysis) Karolinska (Suède)
- Double Digester www (Yale)
- Duke Bioinformatics Shared Resource (TreeMap, ClusterView, GenePlacer, ConduitBrowser, HomoloGeneBrowser, SeqWebHub, BlastWeb ...) Duke (USA)
- DUST filter (Tatusov, Lipman) WUSTL
- Dynafit P. Kuzmic (USA)
- Dynalign (predicting a set of minimal free energy RNA secondary structures common to two sequences) Rochester (USA)
- Dynamite (code generating language developed for sequence comparison) EBI (UK)
- Dynetica (a simulator of dynamic networks) Caltech (USA)
- easyLINKAGE (a PERL script for easy and automated two-/multi-point linkage analyses) Berlin (Allemagne)
- E-CELL (a modeling and simulation environment for biochemical and genetic processes) e-cell (USA)
- EcoCyc: Encyclopedia of E. coli Genes and Metabolism www (Peter Karp and Monica Riley)
- EC_oligos (automated and whole-genome primer design for exons within one or between two genomes) Montreal (Canada)
- EDIBLE (Experimental Design and Information By Likelihood Exploration) EBI (UK)
- Editeurs d'alignement multiple SeaView (France)
- EEGLAB (an interactive Matlab toolbox for processing continuous and event-related EEG data using independent component analysis (ICA) and time/frequency analysis including artifact rejection) UCSD (USA)
- EMBOSS sourceforge
- Emboss perl modules CPAN
- EMBOSS for Windows Blavier
- Eponine (mammalian transcription start sites) Sanger (UK)
- EPPS (Extended Phylogenetic Patterns Search) Witten (Allemagne)
- ERPIN (Easy RNA Profile IdentificatioN) TAGC (France)
- ESPript (multiple sequence alignments in PostScript) IBCP (France)
- ESSA (RNA secondary structure analysis) INRA (France)
- ESTAP (an automated system for the analysis of EST data) Virginia (USA)
- EST analysis tools Bergen (Norvège)
- ESTminer (a Web interface for mining EST contig and cluster databases) Georgia (USA)
- ESTminer (a suite of programs for gene and allele identification) Ames (USA)
- ESTWeb (software package designed for uniform data processing and storage for large-scale EST sequencing projects) Sao Paulo (Brésil)
- ESTate (Expressed Sequence Tag Analysis Tools) EBI (UK)
- ESTprep (preprocessing cDNA sequence reads) Iowa (USA)
- ETV (an application for predicting and visualizing functional sites in protein structures) Houston (USA)
- EvolSimulator (simulation test bed for gene and genome evolution) Halifax (Canada)
- EvoPromoter (finding cis-regulatory modules in Drosophila using phylogenetic hidden Markov models) Sanger (UK)
- Expa (a program for calculating extreme pathways in biochemical reaction networks) California (USA)
- Exonerate (a generic tool for sequence alignment) EBI (UK)
- FADE and PADRE (Atomic Density Methods for Molecular Shape and Shape Complementarity) SDSC (USA)
- FALCON (Fast Assemblies of Large Contigs) www (Harvard)
- FANMOD (a tool for fast network motif detection) Jena (Allemagne)
- Fast and accurate database homology search using upper bounds of local alignment scores Kyoto (Japon)
- FASTA Virginia (USA) (Fasta31t and fasta30t include an html file and two cgi files that simplify setting up a local fasta WWW server)
- Fastml (computing the ancestral amino-acid sequences of a phylogenetic tree) Tel Aviv (Israel)
- FESTA (an efficient comprehensive search algorithm for tagSNP selection using linkage disequilibrium criteria) Michigan (USA)
- FLOSS (flexible ordered subset analysis for linkage mapping of complex traits) Auckland (Nouvelle Zélande)
- Flow Cytometry www (Salk)
- FoldAlign (pairwise local structural alignment of RNA sequences with sequence similarity less than 40%) Frederiksberg (Danemark)
- Folding@home (simulates protein folding ("distributed dynamics")) Stanford (USA)
- Forage (SNP discovery using advanced algorithms and neural networks) Stockholm (Suède)
- Four-Body Scoring Function for Mutagenesis Washington (USA)
- Free Flow Cytometry Software Purdue (USA)
- Free Molecular Modelling Programs MarcSaric
- freqA (identification of putative programmed translational frameshift sites) Utah (USA)
- Friend (an integrated analytical front-end application for bioinformatics) Boston (USA)
- FPV (Fast Protein Visualization Using Java 3D) UCSB (USA)
- FROST (fold recognition program) INRA (France)
- FSSA (a novel method for identifying functional signatures from structural alignments) Washington (USA)
- FUNDER (susceptibility of non-linear systems as an approach to metabolic responses) Madrid (Espagne)
- GAME (detecting cis-regulatory elements using a genetic algorithm) Pennsylvania (USA)
- >GAPWM (a genetic algorithm method for optimizing a position weight matrix) North Carolina (USA)
- Garlic (molecular visualization program, protein structure, DNA structure, PDB, molecular rendering) Osijek (Croatie)
- GASP (Genometric analysis simulation program) NHGRI-NIH (USA)
- GCUA (General Codon Usage Analysis) Maynooth (Irlande)
- GDA (Software for the Analysis of Discrete Genetic Data) Connecticut (USA)
- GDE (linux environment for bioinformatics and evolutionary analysis based on the Genetic Data Environment) Durban (Afrique du Sud)
- GEANFAMMER (GEnome ANalysis and Protein FAMily MakER) MRC (UK)
- GEAR (genomic enrichment analysis of regional DNA copy number changes) Seoul (Corée)
- Gemoda (a generic motif discovery algorithm for sequential data) MIT (USA)
- GENDB (open source genome annotation system) Bielefeld (Allemagne)
- GeneDoc (Multiple Sequence Alignment Editor, Analyser and Shading Utility for Windows) Pittsburgh (USA)
- Gene-finding and Genome-assembly (Twain, Glimmer, GeneZilla, GeneSplicer ..., MUMmer, AMOScmp, Minimus, Bambus ...) Maryland (USA)
- GeneHunter (Imprinting, Modscore, Twolocus) Marburg (Allemagne)
- GeneMachine (integrated tool intended to perform both comparative and predictive gene identification) NHGRI (USA)
- GenePattern (comparative gene marker selection suite) MIT (USA)
- GenePro (a cytoscape plug-in for advanced visualization and analysis of interaction networks) Toronto (Canada)
- GeneRAGE (algorithm for sequence clustering and domain detection) EBI (UK)
- GeneRecon (a coalescent based tool for fine-scale association mapping) Arhus (Danemark)
- GeneSyn (tool for detecting conserved gene order across genomes) Milan (Italie)
- Genetic Analysis Software (FastLink, MSA, CASPAR, PedHunter, CGH, RH Map) NCBI (USA)
- Genetic software (splink, transmit, ped2spl, gh2stat, snphap, tdthap, stata) Cambridge (UK)
- GenRGenS (Generation of Random Genomic Sequences) LRI (France)
- GeneX (Internet available repository of gene expression data) NCGR
- Genexp (tool for simulation of dynamics of genetic regulatory networks) Prague (Czech Republic)
- GenoCluster (accurate automated clustering of two-dimensional data for single-nucleotide polymorphism genotyping by a combination of clustering methods: evaluation by large-scale real data) Tokyo (Japon)
- GenoExpertBacteria (exploration of bacterial genomic, proteic and functional data) INRIA (France)
- GENOME (a rapid coalescent-based whole genome simulator) Michigan (USA)
- GenomeDiagram (genomic and biological sequence schematic drawing package) SCRI (UK)
- GenomeMixer (a complex genetic cross simulator) Tennessee (USA)
- GenRGenS (software for generating random genomic sequences and structures) Orsay (France)
- Gepard (a rapid and sensitive tool for creating dotplots on genome scale) Neuherberg (Allemagne)
- Gepasi (Biochemical simulation) Aberystwyth (Pays de Galles)
- GFF: an exchange format for gene-finding Sanger (UK)
- GFFtools (gff2ps, gff2aplot) Pompeu Fabra (Espagne)
- Ghemical (computational chemistry software package released under the GNU GPL) Kuopio (Finlande)
- GINsim (dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle) Marseille (France)
- GIST-SVM (mismatch string kernels for discriminative protein classification) Columbia (USA)
- GLAD (a system for developing and deploying large-scale bioinformatics grid) Singapore
- GMAP (a genomic mapping and alignment program for mRNA and EST sequences) San Francisco (USA)
- GMOD (Generic Model Organism Database Construction Set) USDA-NIH (USA)
- GNA (tool for the modeling and simulation of genetic regulatory systems) INRIA (France)
- GOAT (Genome Organization Analysis Tool) Virginia (USA)
- GOLD (Graphical Overview of Linkage Disequilibrium) Oxford (UK)
- GPRIME (PCR primers tools) ANU (Australie)
- GRAMM (program for protein docking) Kansas (USA)
- Grappe (fast searching a text file for regular expressions) Loria (France)
- GRASP (Graphical Representation and Analysis of Structural Properties) Columbia (USA)
- GRAST (a new way of genome reduction analysis using comparative genomics) Maynooth (Irlande)
- GRIL (genome rearrangement and inversion locator) Wisconsin-Madison (USA)
- GSC software (Polybayes, Miropeats, GASP) WUSTL (USA)
- GSCANDB software (management, presentation and interpretation of genome scans) Oxford (UK)
- GSEA-P (a desktop application for Gene Set Enrichment Analysis) MIT (USA)
- GUS (Genomics Unified Schema) CBIL (USA)
- GWAsimulator (a rapid whole-genome simulation program) Pennsylvania (USA)
- GXNA (gene expression network analysis and applications to immunology) Stanford (USA)
- HAPLOPOOL (improving haplotype frequency estimation through DNA pools and phylogenetic modeling) Berkeley (USA)
- HapBlock (haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms) Alabama (USA)
- HaploPainter (a tool for drawing pedigrees with complex haplotypes) Berlin (Allemagne)
- Haploview (analysis and visualization of LD and haplotype maps) Cambridge (USA)
- HapMiner (aplotype-based linkage disequilibrium mapping via direct data mining) California (USA)
- HelixCorr (co-evolving residues in membrane proteins) Freising (Allemagne)
- HMM (PASSML and PASSML-TM) EBI (UK)
- HMMCOMP (Comparison of hidden Markov models) Aarhus (Danemark)
- HMMER Washington (USA)
- HMMER (mpiblast, clustalx ..) Scalable informatics
- HomologMiner (looking for homologous genomic groups in whole genomes) Penn State (USA)
- HONIG Lab software (DelPhi, MCCE, Energy functions, SCAP, Loopy, Spin-PP, GRASP, GRASS,..) Columbia (USA)
- Html4blast Pasteur
- HTS-Corrector (software for the statistical analysis and correction of experimental high-throughput screening data) Montreal (Canada)
- i-ADHoRe 2.0 (an improved tool to detect degenerated genomic homology using genomic profiles) Ghent (Belgique)
- ICM-Browser (structural biology) MolSoft
- Imagene Notebook (cooperative computer environment for the annotation and analysis of genomic sequences) Jussieu (France)
- IMEx (Imperfect Microsatellite Extractor) Hyderabad (Inde)
- IML (prediction of RNA Secondary Structures with Pseudoknots) Washington (USA)
- IMP services (GPI predictor, SSCP, NSC,..) IMP (Autriche)
- INCA (synonymous codon usage analysis and clustering by means of self-organizing map) Zagreb (Croatie)
- Indelign (a probabilistic framework for annotation of insertions and deletions in a multiple alignment) Illinois (USA)
- Infernal (inference of RNA secondary structure alignments) Washington (USA)
- INFO-RNA (a fast approach to inverse RNA folding) Freiburg (Allemagne)
- Ingenenue (Genetic Network Construction Software) NSF (USA)
- IntegraGen (open source package for molecular biology) urbigene
- Intergenic sequence inspector (searching and identifying bacterial RNAs) Rennes (France)
- InterProScan Package EBI (UK), voir aussi
- Intersect (identification and visualization of overlaps in database search results) UCSF (USA)
- InterViewer (visualizing large-scale protein interaction networks in the three-dimensional space) Inchon (Corée)
- IRILmap (linkage map distance conversion software for intermated recombinant inbred lines) INRA (France)
- I-sites (method for predicting the local structure of a protein from its amino acid sequence) RPI (USA)
- Jade development environment and demos CSHL (USA)
- JaDis (computing distances between nucleic acid sequences) PBIL (France)
- Jalview (a java multiple alignment editor) Dundee (UK)
- Java-based Molecular Biology Work Bench EMBL (Alignment Editor, Pattern Searching, PCR, pI, Oligo, Map, Translate, ..)
- JCell (a Java-based framework for inferring regulatory networks from time series data) Tübingen (Allemagne)
- Jeff's Perl Programs CWRU (USA)
- JESAM (CORBA software components to create and publish EST alignments and clusters) EBI (UK)
- JigCell Model Builder and Run Manager Virginia (USA)
- JIGSAW (integration of multiple sources of evidence for gene prediction) Maryland (USA)
- Jnet (Neural Network Protein Secondary Structure Prediction Method) Dundee (UK)
- JTEF (3' terminal exon finder for human DNA sequences) CSHL (USA)
- KAlignmentViewer (Qt interface for the display and browsing of multiple sequence alignments) EBI (UK)
- KDD (feature selection and transduction for prediction of molecular bioactivity for drug design : matlab) Tuebingen (Allemagne)
- KGML-ED (dynamic exploration and editing of KEGG pathway diagrams) Gatersleben (Allemagne)
- KGraph (a system for visualizing and evaluating complex genetic associations) Michigan (USA)
- Kinetikit (adaptive stochastic-deterministic chemical kinetic simulations) Bangalore (Inde)
- KtreeDist (quantification of differences in the relative branch length and topology of phylogenetic trees) Barcelone (Espagne)
- LDAba (java-based linkage disequilibrium analyzer) CAMS (Chine)
- LDDist (Perl module for calculating LogDet pair-wise distances for protein and nucleotide sequences) Uppsala (Suède)
- LBDOT(rapid and sensitive dot-matrix methods for genome analysis) Lynnon (Canada)
- LdCompare (rapid computation of single- and multiple-marker r2 and genetic coverage) California (USA)
- LDMAP (exploiting large scale computing to construct high resolution linkage disequilibrium maps of the human genome) Southampton (UK)
- LFM-Pro (a tool for detecting significant local structural sites in proteins) Ankara (Turquie)
- LGBC-programmes (Macintosh 1988 V.F.) www
- LIGPLOT (program for automatically plotting protein-ligand interactions) BSM (UK)
- Linkage Analysis Sever NIH (USA)
- Linkage Analysis Softwares list Rockfeller (USA)
- LNP (identifying Coexpressed ESTs) Palo Alto (USA)
- Logiciels de BIA (Statistiques, Biologie moléculaire) INRA (France)
- Loki (MCMC Linkage Analysis for Large Pedigrees) Washington (USA)
- Look-Align (an interactive web-based multiple sequence alignment viewer with polymorphism analysis support) CSHL (USA)
- LSA (application of latent semantic analysis to protein remote homology detection) Harbin (Chine)
- LUA (method for estimating ancestral amino acid composition and its application to proteins of the Last Universal Ancestor) Princeton (USA)
- LVB (reconstructing evolution with parsimony and simulated annealing) St Andrews (UK)
- MACAW (program for locating, analyzing, and editing blocks of localized sequence similarity) NCBI (USA)
- MacOS X scientific applications FSNET, voir aussi MacScience
- MacroModel www (An Integrated Software System for Modeling Organic and Bioorganic Molecules Using Molecular Mechanics)
- MacStripe (Prediction of Coiled Coils) York (UK)
- MAFFT (multiple sequence alignment program) Fukuoka (Japon)
- MAGPIE (Automated Genome Project Investigation Environment) Rockfeller (USA), voir aussi Calgary (Canada)
- Make2D-DB II Package (to create, convert, interconnect and keep up-to-date 2-DE databases) Expasy (Suisse)
- MAMMOT (a set of tools for the design, management and visualization of genomic tiling arrays) Cambridge (UK)
- Manatee (a web-based gene evaluation and genome annotation tool) Sourceforge
- MANTIS (a phylogenetic framework for multi-species genome comparisons) Bruxelles (Belgique)
- Map Manager (program for a Macintosh which helps analyze the results of genetic mapping experiments using backcrosses, intercrosses, or recombinant inbred(RI) strains DCMB (USA)
- Mapper Illinois (USA)
- Maptools (programs for working with experimental three-dimensional (density) maps) Gottingen (Allemagne)
- Martin group software (mlstdbNet, START, Sequence comparator) Oxford (UK)
- MASS (Multiple Alignment by Secondary Structures) TAU (Israel)
- MassXpert (predicting and analysing mass spectrometric data) Bordeaux (France), voir aussi PolyXmass
- MASTR (multiple alignment and structure prediction of non-coding RNAs using simulated annealing) Copenhague (Danemark)
- MatCompare (methods for comparing transcription factor binding site (TFBS) position frequency matrices (PFMs)) CSHL (USA)
- MatInd et MatInspector, ConsInd et ConsInspector, GenomeInspector, etc. BIODV (to derive a matrix description of a consensus and to detect consensus matches in nucleotide sequence data, ORF ..) (Allemagne)
- MatrixReduce (statistical mechanical modeling of genome-wide transcription factor occupancy data) New York (USA)
- Mauve (Multiple Genome Alignment) Wisconsin (USA)
- MAVG (locating non-overlapping maximum average segments in a given sequence) Iowa (USA)
- McCaskill-MEA (robust prediction of consensus secondary structures using averaged base pairing probability matrices) Tokyo (Japon)
- McClellan Lab Software (TreeSAAP, DataConvert, CDM, CDSParser, AlignmentHelper, SimSeq) BYU (USA)
- MCMCSALUT (Markov Chain Monte Carlo Sequence Alignment Utility) Francfort (Allemagne)
- MC-SYM (Prédiction de structure 3D d'acides nucléiques) MC-SYM (Canada)
- MCell (A General Monte Carlo Simulator of Cellular Microphysiology) Salk Institute (USA), autre lien
- Mclip (motif detection based on cliques of gapped local profile-to-profile alignments) Canberra (Australie)
- MED-Start (for identifying translation initiation sites in microbial genomes) Nanjing (Chine)
- MEGA (Molecular Evolutioary Genetics Analysis) Megasoftware
- MEMSAT (prediction of the secondary structure and topology of all-helix integral membrane) UCL (PC seulement) (UK)
- Metabolic Control Analysis (Scamp, Metacon, Empath, Metatool) Oxford (UK)
- Metabolic tools (METATOOL, BlockDiag, OptiMode, Separator) Jena (Allemagne)
- MetaFluxNet (management of metabolic reaction and metabolic flux analysis) MBEL (Korea)
- metaSHARK (software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella) Leeds (UK)
- Metatool 5.0 (fast and flexible elementary modes analysis) Jena (Allemagne)
- Microarray
- ACE-it (a tool for genome-wide integration of gene dosage and RNA expression data) Amsterdam (The Netherlands)
- aCGH-Smooth (tool for the analysis of array Comparative Genomic Hybridization (array-CGH) data) Amsterdam (The Netherlands)
- Affymetrix tools (CHPReader, GenePicker) Milan (Italie)
- AffyR (package to use oligonucleotide microarrays data) CBS (Danemark)
- AGScan (a pluggable microarray image quantification software based on the ImageJ library) INRA (France)
- AMADA (Analyzing Microarray Data) Ottawa (Canada)
- An application for assessing quality of RNA hybridized to Affymetrix GeneChips Virginia (USA)
- ArrayCluster (an analytic tool for clustering, data visualization and module finder on gene expression profiles) Tokyo (Japon)
- ArrayDB Software NHGRI (USA)
- ArrayExpress Software EBI (UK)
- BagBoosting (for Tumor Classification with Gene Expression Data) Zurich (Suisse)
- Base (manage the massive amounts of data generated by microarray analysis) Lund (Suède)
- BGX (flexible Bayesian clustering and partition models for gene expression data) Londres (UK)
- Bioconductor Harvard (USA), voir aussi Bioconductor Packages
- BNArray (an R package for constructing gene regulatory networks from microarray data by using Bayesian network) Hangzhou (Chine)
- Boosting for tumor classification with gene expression data ETHZ (Suisse)
- BRB ArrayTools NCI (USA)
- CGHcall (calling aberrations for array CGH tumor profiles - R package) Amsterdam (The Netherlands)
- ChARM (accurate detection of aneuploidies in array CGH and gene expression microarray data) Princeton (USA)
- ChromoViz (R package for multimodal visualization of microarray data, DNA copy number alterations...) Seoul (Republic of Korea)
- ClaNC (classification of microarrays to nearest centroids) Washington (USA)
- Clans (analyzing microarray data) Canberra (Australie)
- Clusterv (a tool for assessing the reliability of clusters discovered in DNA microarray data - R package) Milan (Italie)
- CoCo (a web application to display, store and curate ChIP-on-chip data integrated with diverse types of gene expression data) Heidelberg (Allemagne)
- CPAS (computational proteomics analysis system) FHCRC (USA)
- CRC (clustering microarray gene expression data using weighted Chinese restaurant process) Michigan (USA)
- Dapple (image analysis software) Washington (USA)
- DBmcmc (inferring genetic regulatory interactions from microarray gene expression data) Edinburgh (UK)
- dChipSNP (significance curve and clustering of SNP-array-based loss-of-heterozygosity data) Harvard (USA)
- DNC-MIX (Class discovery and classification of tumor samples using mixture modeling of gene expression data-a unified approach) Ohio (USA)
- Doelan (a solution for quality control monitoring of microarray production) ENS (France)
- Dual-genome (primer design for construction of DNA microarrays) Stockholm (Suède)
- EDGE (extraction and analysis of differential gene expression) Washington (USA)
- eQTL Explorer (integrated mining of combined genetic linkage and expression experiments) Londres (UK)
- FARMS (R package for Factor Analysis for Robust Microarray Summarization) Linz (Autriche)
- FGDP ( Functional Genomics Data Pipeline) Philadelphia
- FindGDPs (identification of primers for labeling microbial transcriptomes for DNA microarray analysis) Texas (USA)
- FIVA (functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes) Groningen (The Netherlands)
- FSPMA (a friendly statistics package for microarray analysis) Cambridge (UK)
- GAAS (Gene Array Analyzer Software) Milan (Italie)
- GandrKB (ontological microarray annotation and visualization) Berlin (Allemagne)
- GARBAN (genomic analysis and rapid biological annotation of cDNA microarray and proteomic data) Pamplona (Espagne)
- GATC platform (Ven Mapper, GO Mapper, ..) Rotterdam (The Netherlands)
- GEMS (evaluation of multicategory classification methods for microarray gene expression cancer diagnosis) Nashville (USA)
- GeneMerge (post-genomic analysis, data mining, and hypothesis testing) Harvard (USA)
- GeneNetwork (an interactive tool for reconstruction of genetic networks using microarray data) Taipei (Tawain)
- Genomics Software (Gene Pattern, Cluster, Cruiser) MIT (USA)
- Genome-scale oligonucleotide design for microarrays Michigan (USA)
- GenMAPP (application designed to visualize gene expression data on maps representing biological pathways and groupings of genes) Gladstone Institutes (USA)
- Gesses (Evolutionary algorithms for finding optimal gene sets in microarray prediction) UCSC (USA)
- GIMM (bayesian mixture model based clustering of replicated microarray data) Cincinnati (USA)
- GLR (a statistical analysis program to identify differentially expressed genes) Utah (USA)
- GoMiner (tool for biological interpretation of 'omic' data) NCI (USA)
- GridGrinder (automated image analysis for microarrays) SourceForge
- GRNInfer (inferring gene regulatory networks from multiple microarray datasets) Missouri (USA)
- Hierarchical Clustering Explorer for Multidimensional Clustering and Outlier Detection Maryland (USA)
- HiRes (a tool for comprehensive assessment and interpretation of metabolomic data) Columbia (USA)
- HMM-Kalign (a tool for generating sub-optimal HMM alignments) Gif sur Yvette (France)
- HykGene (a hybrid approach for selecting marker genes for phenotype classification using microarray gene expression data) Hanover (USA)
- Ideogram browser (visualization of genomic aberrations using Affymetrix SNP arrays) Ulm (Allemagne)
- IGG (tool to integrate GeneChips for genetic studies) Hong Kong (Chine)
- I/NI-calls (for the exclusion of non-informative genes: a highly effective filtering tool for microarray data / R-package) Linz (Autriche)
- Integrative Array Analyzer (a software package for analysis of cross-platform and cross-species microarray data) California (USA)
- INTERALIGN (interactive alignment editor for distantly related protein sequences) Bagnols-sur-Cèze (France)
- limmaGUI (a graphical user interface for linear modeling of microarray data) Parkville (Australie)
- LAP (to identify differentially expressed chromosomal regions) Padoue (Italie)
- Libaffy (software for processing Affymetrix(R) GeneChip(R) data) South Florida (USA)
- MACGT (multi-dimensional automated clustering genotyping tool for analysis of microarray-based mini-sequencing data) Vancouver (Canada)
- Machaon (an integrated tool for microarray data clustering and cluster validity assessment) Dublin (Irlande)
- MADGE (scalable distributed data management software for cDNA microarrays) Floride (USA)
- Magic Tools (integrated microarray data analysis) Davidson (USA)
- Max Planck (Allemagne) (MACAT, Stam, compdiagTools)
- MAIA (package for automatic microarray image analysis) Institut Curie (France)
- maSigPro (a method to identify significantly differential expression profiles in time-course microarray experiments) Valence (Espagne)
- MASQOT-GUI (spot quality assessment for the two-channel microarray platform) Umea (Suède)
- MBR (microarray blob-defect removal improves array analysis) Harvard (USA)
- MDAT (for normalization, adjustment and analysis of gene expression data) Oklahoma (USA)
- matchprobes (a Bioconductor package for the sequence-matching of microarray probe elements) Heidelberg-Boston
- MGED Software (Microarray Gene Expression) MGED
- Maxd Manchester
- MaxMinCluster (algorithm for aligning two whole genomes) Hong Kong
- mdclust (Exploratory Microarray Analysis by Multidimensional Clustering) Munich (Allemagne)
- Microarray data mining with visual programming Ljubljana (Slovénie)
- Microarray softwares MRC (UK)
- MPP (a microarray-to-phylogeny pipeline for analysis of gene and marker content datasets) Norwich (UK)
- MSBE (computing the maximum similarity bi-clusters of gene expression data) Hong Kong
- NMPP (a user-customized NimbleGen microarray data processing pipeline) Yale (USA)
- OligoWiz (performs intelligent design of oligonucleotides for DNA microarrays) CBS (Danemark)
- OLIN (optimized normalization, visualization and quality testing of two-channel microarray data) Berlin (Allemagne)
- Oliz (Perl scripts that selects 50mer oligonucleotides for use in DNA microarrays) UTMEM (USA)
- Ontologizer (an XML-based Java application provides a function-oriented overview of the results of cluster analysis of gene-expression) Berlin (Allemagne)
- P-Scan (Microarray : Peak quantification using Statistical Comparative ANalysis) NIH (USA)
- Pathway analysis using random forests classification and regression Yale (USA)
- PATIKA ((Pathway Analysis Tool for Integration and Knowledge Acquisition)) Ankara (Turquie)
- Plato (robust cluster analysis of microarray gene expression data) Georgia (USA)
- ProMAT (protein microarray analysis tool) Richland (USA)
- Quantum clustering (Mathlab) Tel Aviv (Israel)
- R code for the empirical Bayes Madison (USA)
- R package (Statistics for Microarray Analysis) Berkeley
- YASMA Birbeck
- Rosetta (learning rule-based models of biological process from gene expression time profiles using Gene Ontology) Trondheim (Norvège)
- R Packages For Gene Expression Analysis (links) Munich
- R-Web Glasgow (UK)
- SeqExpress (desktop analysis and visualization tool for gene expression experiments) Cambridge (UK)
- SignalViewer (application for image analysis) FHCRC (USA)
- Spot shape modelling and data transformations (R source code) Frederiksberg (Danemark)
- TAPPA (topological analysis of pathway phenotype association) Wisconsin (USA)
- THEA (ontology-driven analysis of microarray data) Nice (France)
- TileMap (creates chromosomal map of tiling array hybridizations) Stanford (USA)
- tRMA (tools for R Microarray Analysis) CSIRO
- Variational Bayesian mixture modelling framework for cluster analysis of gene-expression data Cambridge (UK)
- Venn Mapping (clustering of heterologous microarray data based on the number of co-occurring differentially expressed genes) Rotterdam (The Netherlands)
- Microarray analysis and database softwares comparison YLF
- Microbiological software (MSDOS) Southampton (UK)
- MIG software (Frost, Island, MuGeN, R'Hom, R'Mes) INRA (France)
- Migrate (comparison of Bayesian and maximum-likelihood inference of population genetic parameters) Florida (USA)
- mILD (a tool for constructing and analyzing matrices of pairwise phylogenetic character incongruence tests) New York (USA)
- MINER (software for phylogenetic motif identification) California (USA)
- MIRA 2 (Genome Shotgun and EST Sequence Assembler) Chevreux
- Miropeats (sequence similarity amongst any set of DNA sequences) Oklahoma (USA)
- MitoPred (genome-scale method for predicting mitochondrial proteins) Albany (USA)
- MLR-tagging (informative SNP selection for unphased genotypes based on multiple linear regression) Georgia (USA)
- MMTK (Molecular Modelling Toolkit) Orléans (France)
- MMTSB software (Modelling package, Charm, Tool set, Yammp) SRI (USA)
- Möbius (an integrated discrete-event modeling environment) Illinois (USA)
- Modélisation génétique et moléculaire (R'MES, R'PRO, SliceEMBL, SeqFold) SSB (France)
- Modeller (program for homology protein structure modelling by satisfaction of spatial restraints) California (USA)
- MoDisc (bayesian-based selection of metabolic objective functions) Connecticut (USA)
- Modular, scriptable and automated analysis tools for high-throughput peptide mass fingerprinting Halmstad (Suède)
- ModView (visualization of multiple protein sequences and structures) California (USA)
- MOIL (modeling package to simulate structure, dynamics, and function of biological molecules) Cornell (USA)
- MOLDEN (a pre- and post processing program of molecular and electronic structure) CMBI (Pays-Bas)
- MOLDY (molecular dynamics simulation) Oxford (UK)
- Molecular Biology related programs for Linux BioInf
- Molecular Genetics Analysis ((2LD, EH, GeneCounting, Discord, Gemini, ..) Cambridge (UK)
- Molecular Neurobiology (Melting, Cosindex, Compacc, Clu2nssp) Pasteur (France)
- Molekel (molecular visualization package) CSCH (Suisse)
- MolFit (protein-protein docking) Rehovot (Israel)
- MolMol (MOLecule analysis and MOLecule display) ETHZ (Suisse)
- MOLPHY (Computer Program Package for Molecular Phylogenetics) Tokyo (Japon)
- Molscript Avatar
- Moma (analysis of optimality in natural and perturbed metabolic networks) Harvard (USA)
- MotifRank (computing exact P-values for DNA motifs) Beijing (Chine)
- MPEx (Membrane Protein Explorer) Irvine (USA)
- mpiBLAST (open source parallelization of NCBI BLAST) LANL (USA)
- MPSA (Multiple Protein Sequence Analysis) PBIL (France)
- MrBayes (Bayesian inference of phylogeny) Florida (USA)
- MREPS (finding tandem repeats) IFL (France)
- MSFACTs (Metabolomics Spectral Formatting and Conversion Tools) Ardmore (USA)
- msHOT (modifying Hudson's ms simulator to incorporate crossover and gene conversion hotspots) Chicago (USA)
- MSQT (for choosing SNP assays from multiple DNA alignments) Tubingen (Allemagne)
- MSS (whole genome alignment using a mutation sensitive approach) Hong Kong (Chine)
- MSTAT (nonparametric statistical methods) Wisconsin (USA)
- MTOM (network neighborhood analysis with the multi-node topological overlap measure) California (USA)
- Mtreemix (a software package for learning and using mixture models of mutagenetic trees) Saarbrucken (Allemagne)
- MuGeN (simultaneous exploration of multiple genomes and computer analysis results) INRA (France)
- MulBlast (gathering BLAST pairwise alignments in one multiple alignment) Montpellier (France)
- MultiParanoid (automatic clustering of orthologs and inparalogs shared by multiple proteomes) Stockholm (Suède)
- MultiPLX (automatic grouping and evaluation of PCR primers) Tartu (Estonie)
- Multi-Q (web server for multiplexed protein quantitation) Taipei (Taiwan)
- Multivariate analysis and graphical display software package for Macintosh and PC (NetMul, MacMul, GraphMu, MacDendro, ADE-4) Lyon (France)
- Multivariate analysis software Oklahoma (USA)
- MUMmer (utra-fast alignment of large-scale DNA and protein sequences) Baltimore (USA)
- MUSCLE (multiple alignment program for protein sequences) California (USA)
- MUTAGEN (Multi-User Tool for Annotating GENomes) Copenhague (Danemark)
- Mview (tool for converting the results of a sequence database search into the form of a coloured multiple alignment) NIMR (UK)
- MyWEST (My Web Extraction Software Tool for effective mining of annotations from web-based databanks) Milan (Italie)
- MZmine (toolbox for processing and visualization of mass spectrometry based molecular profile data) Espoo (Finlande)
- Naccess (Atomic Solvent Accessible Area Calculations) UMIST (UK)
- NAMOT (Nucleic Acid MOdeling Tool) www (Los Alamos)
- NBmiRTar (Naïve Bayes for microRNA target predictions-machine learning for microRNA targets) Philadelphia (USA)
- Nemo (an evolutionary and population genetics programming framework) Lausanne (Suisse)
- NestedMICA (a method for discovering over-represented short motifs in large sets of strings - typical applications include finding candidate transcription factor binding sites in DNA sequences) Sanger (UK)
- Nestor3D (generation of 3D templates of active sites of proteins with rigid prosthetic groups) Kingston (UK)
- NetMatch (a Cytoscape plugin for searching biological networks) Catania (Italie)
- NCList (algorithm for accelerating interval query of genome alignment and interval databases) California (USA)
- NJplot (tree drawing program) PBIL (France)
- NetBuilder (graphical tool for representing and simulating genetic regulatory networks) Hertfordshire (UK)
- Network Motif Software (efficient sampling algorithm for estimating subgraph concentrations and detecting network motifs) Weizmann (Israel)
- Neural Networks at your Fingertips Geocities (USA)
- Neural Simulation Language NSL
- NEURON (simulator of neurons and networks) North Carolina (USA)
- Ngila (global pairwise alignments with logarithmic and affine gap costs) Carolina (USA)
- NovoHMM (semi-supervised LC/MS alignment for differential proteomics) ETHZ (Suisse)
- NvAssign (protein NMR spectral assignment with NMRView) NIH (USA)
- OligoPicker (selecting up to five oligo probes for each of the DNA sequences you provided for microarray spotting) Harvard (USA)
- OmicBrowse (a browser of multidimensional omics annotations) RIKEN (Japon)
- OMWSA (detection of DNA repeats using moving window spectral analysis) Sydney (Australie)
- ONDEX (graph-based analysis and visualization of experimental results) Harpenden (UK)
- Open Bioinformatics Foundation (BioPerl, BioJava, BioPython, BioPipe, BioSQL, etc..) OBF
- Open Lab (open sources bioinformatics) OSBR, voir aussi piper project
- Open Molecule Foundation (Applets and Java packages for the bio- and chemo- informatics communities) ICSTM (UK)
- OpenMMS Toolkit (Corba, Relation Database and XML Software for Macromolecular Structure) SDSC (USA)
- The Open Science Project (dedicated to writing and releasing free and Open Source scientific software) OpenScience (USA)
- Open source clustering software Tokyo (Japon)
- Operon prediction without a training set Washington (USA)
- Optimizer (a Bayesian scoring function approach to motif discovery) Harvard (USA)
- Optimizing Substitution Matrix by Separating Score Distributions Tokyo (Japon)
- ORF-Curator (molecular curation of genes and gene clusters in prokaryotic organisms) Columbia (USA)
- ORI-GENE (tool for Gene Classification Based on the Evolutionary Tree) Fukuoka (Japon)
- ORILOC (prediction of replication boundaries in unannotated bacterial chromosomes) PBIL
- ORNL Tools (Prospect, Excavator, Domain Parser, Primegens) ORNL (USA)
- ORPHEUS (gene prediction in complete bacterial genomes and large genomic fragments) MIPS (Allemagne)
- OWEN (hierarchical approach to aligning collinear regions of genomes) NCBI (USA)
- Packages for life science MathSource (USA)
- PAL (Java library for researchers in molecular phylogenetics) Pal-project
- Palingol Jussieu (France)
- Paloverde (an OpenGL 3D phylogeny browser) California (USA)
- PAML (Phylogenetic Analysis by Maximum Likelihood) UCL (UK)
- Panta rhei (QAlign2) (an open graphical environment for sequence analysis) Bielefeld (Allemagne)
- Paquetages Debian de biologie debian.org (France)
- Parallel multifactor dimensionality reduction: a tool for the large-scale analysis of gene-gene interactions Nashville (USA)
- PARIS (a proteomic analysis and resources indexation system) Jouy-en-Josas (France)
- PARS (Positional Analysis of Regulatory Sequences) Hertfordshire (UK)
- PartiGene (constructing partial genomes) Edinburgh (UK)
- PartTree (an algorithm to build an approximate tree from a large number of unaligned sequences : part of MAFFT) Fukuoka (Japon)
- PCMA (fast and accurate multiple sequence alignment based on profile consistency) Texas (USA)
- Pcons5 (combining consensus, structural evaluation and fold recognition scores) Stockholm (Suède)
- PCP (a program for supervised classification of gene expression profiles) California (USA)
- PDAP (phenotypic diversity analysis programs) California (USA)
- PDB2PQR (expanding and upgrading automated preparation of biomolecular structures for molecular simulations) Washington (USA)
- pDRAW32 (DNA analysis software : PC) AcaClone
- PEDSTATS (descriptive statistics, graphics and quality assessment for gene mapping data) Michigan (USA)
- Pegasys (software for executing and integrating analyses of biological sequences) Vancouver (Canada)
- PEGR (Phylogenetic exploration of bacterial genomic rearrangements) Toulouse (France)
- PepSplice (cache-efficient search algorithms for comprehensive identification of tandem mass spectra) ETHZ (Suisse)
- PERCH NMR Software Kuopio (Finlande)
- Perl as a Tool for Linkage Analysis Rockfeller (USA)
- Perl Modules for Molecular Chemistry PerlMol
- PerlPrimer (open-source PCR primer design) sourceforge
- PermutMatrix (a graphical environment to arrange gene expression profiles in optimal linear order) Montpellier (France)
- PG (an efficient, versatile and scalable pattern growth approach to mine frequent patterns in unaligned protein sequences) Amsterdam (The Netherlands)
- PGE soft (gBioSeq, Treeplot, Populations, Nuées, TFSEQ, LEA) Gif sur Yvette (France)
- PHIRE (a deterministic approach to reveal regulatory elements in bacteriophage genomes) Leuven (Belgique)
- Phrap and Phred (Fast sequence assembly) Phrap (USA)
- Phyloclus (combining phylogenetic motif discovery and motif clustering to predict co-regulated genes - perl programs) Pennsylvania (USA)
- Phylocomposer and phylodirector (analysis and visualization of transducer indel models) Berkeley (USA)
- PhyloGena (a user-friendly system for automated phylogenetic annotation of unknown sequences) Bremerhaven (Allemagne)
- Phylogénie, évolution ...
- ALTree (association detection and localization of susceptibility sites using haplotype phylogenetic trees) Villejuif (France)
- APE (Analyses of Phylogenetics and Evolution in R language) Montpellier
- Auckland (Pebble including sUPGMA)
- California (HyPhy : maximum likelihood analyses)
- Connecticut
- Sanger (UK)
- Glasgow, voir aussi
- Hennig (Parsimony Analysis Software)
- Ilinois (fastDNAml)
- Iowa (Rainbow, Quartet Suite, MRF Heuristic Supertree)
- Iowa (Diverge, GeneContent, Mgenome, NetDyn)
- LANL (Weighbor: weighted version of Neighbor Joining)
- LMS (PAUP)
- Lyon (NetMul, MacMul, GraphMu, MacDendro, ADE-4)
- Manchester (PHASE : Phylogenetics and Sequence Evolution)
- MEP
- Montréal (Canada) (T-REX : Tree and Reticulogram reconstruction)
- Montpellier (PHYML, MSALIGN, QR2, BioNJ, Q*, Gamma, DTscore, FastME, Model Trees)
- Oxford (UK) (Unix, Macintosh)
- Pasteur (Taxotron software for Macintosh)
- PennState
- Pusan (Phylodraw)
- Stockholm (galaxie : CGI scripts for sequence identification through automated phylogenetic analysis)
- Sydney (Australie) (TreeCons, Hetero, BH, SeqVis, DMP, Symtest, BH+I, Homo)
- UCLA (BAli-Phy : simultaneous Bayesian inference of alignment and phylogeny) (USA)
- Vigo (Espagne) (TreeScan, ProtTest, ModelTest, TCS, Geodis, SNPSim, Collapse)
- Washington, voir aussi ATV
- Phylogenetic Tree Reconciler Lyon (France)
- PhyloGrapher (Graph Visualization Tool) Davis, voir aussi ATGC (USA)
- Phylo_win (molecular phylogenetic inference) PBIL (France)
- PhylPro (detects genetic recombinations in homologous sequences) ANU (Australie)
- PipTools Software Package (alignments of similar regions in two DNA sequences) Pensylvania (USA)
- PIANA (protein interactions and network analysis) Barcelone (Espagne)
- pIPHULA (parallel inference of population parameters using a likelihood approach) Vienne (Autriche)
- PIVOT (protein interactions visualization tool) Tel Aviv (Israel)
- pknotsRG (RNA pseudoknot folding including near-optimal structures and sliding windows) Bielefeld (Allemagne)
- Plasmid Processor (W 95) Kuopio (Finlande)
- PMcomp/PMmulti (alignment of structural RNAs) Vienne (Autriche)
- POCs (Pox Virus Orthologous Clusters) Victoria (Canada)
- PolyXmass (mass spectrometric data analysis) Polyxmass
- PovChem (molecular graphics) Johns Hopkins (USA)
- PowerCore (a program applying the advanced M strategy with a heuristic search for establishing core sets) Suwon (Malaisie)
- PowQ (a user-friendly package for the design of variance component multipoint linkage analysis studies) Londres (UK)
- PPH (perfect phylogeny haplotyper: haplotype inferral using a tree model) California (USA)
- Pre-amyl (Identification of amyloid fibril-forming segments based on structure and residue-based statistical potential) Beijing (Chine)
- PREPI (molecular graphics program) BMM (UK), voir aussi SBGI
- Primer MIT (USA)
- PrISM.1 (Protein Informatics System for Modeling) Columbia (USA)
- PROCHECK (checks the stereochemical quality of a protein structure) UCL (UK)
- ProfDist (a tool for the construction of large phylogenetic trees based on profile distances) Wurzburg (Allemagne)
- ProMoT/Diva (modular modeling of cellular systems) Magdeburg (Allemagne)
- Promoter Extraction from GenBank (PEG) CSHL
- PROMSCAN (predicts sigma54-dependent promoters) uklinux
- PROSEQ (equence editing and population genetics, (mol/evol) analysis) Edinburgh (UK)
- ProServer (a simple, extensible Perl DAS server) Sanger (UK)
- ProSMoS (searching for three-dimensional secondary structural patterns in proteins ) Texas>/A> (USA)
- PROSPECT (PROtein Structure Prediction and Evaluation Computer Toolkit) ORNL (USA)
- ProteinScope (Free viewer for RCSB Protein Data Bank* files) www
- PROTMAP2D (visualization, comparison and analysis of 2D maps of protein structure) Varsovie (Pologne)
- ProViz (protein interaction visualization and exploration) Bordeaux (France)
- PSC tools (protein structure comparison by probability-based matching of secondary structure elements) Taipei (Taiwan)
- PseudoPipe (an automated pseudogene identification pipeline) New Haven (USA)
- PSIPRED (Secondary structure prediction) UCL (UK)
- PSTAGs (for aligning and predicting RNA secondary structures including a simple type of pseudoknot) Yokohama (Japon)
- PTG (a parsimonious tree-grow method for haplotype inference) Beijing (Chine)
- PubCrawler - an Update Alerting Service for PubMed and GenBank : perl script PubCrawler
- Publicly Available Software (ESTPrep, RHScorer, Clustering, UITagCreator) CLCG (USA)
(USA)
- PUNS (transcriptomic- and genomic-in silico PCR for enhanced primer design) Toronto (Canada)
- PyMOL (molecular modeling system) sourceforge
- PySCeS (Python Simulator for Cellular Systems) Matieland (Afrique du Sud)
- Python base software MGL (USA)
- Python-based software for life science research BioPython (USA)
- Python to solve problems in bioinformatics (calculating gene regulatory networks from gene expression data) Tokyo (Japon)
- pyzerg (python wrapper for the Zerg BLAST parser) Dundee (Ecosse)
- QAlign (quality-based multiple alignments with dynamic phylogenetic analysis) Bielefeld (Allemagne)
- QFC (Quasi-Periodic Feature Classifier algorithm for G protein-coupled receptors) Pennsylvania (USA)
- QTDT (Linkage Disequilibrium Analyses for Quantitative Traits) Michigan (USA)
- QTL Cartographer (a suite of programs to map quantitative traits using a map of molecular markers) North Carolina (USA)
- QTLNetwork 2.0 (mapping the genetic architecture of complex traits in experimental populations) Zhejiang (Chine)
- QTree (a program for generating CPK) UCL (UK)
- QuDA (the Qualitative Data Analysis Tool) Dresden (Allemagne)
- R/qtl (a QTL mapping environment) Johns Hopkins (USA)
- R'MES (Programs to Find Words with Unexpected Frequencies in DNA Sequences) INRA (France)
- Range and Nemo (synthetic microarray data generation with RANGE and NEMO) Fairbanks (USA)
- Rankgene (a program to rank genes from expression data) Boston (USA)
- RAPDistance Package ANU (Australie)
- Rapid (fast DNA database searching) Manchester (UK)
- RASCAL (rapid scanning and correction of multiple sequence alignments) Strasbourg (France)
- RasMol Berkeley, voir aussi UMass, voir aussi Open RasMol
- RAT (a program for the high-throughput detection of recombination) Norwich (UK)
- RAVENNA (software package for non-coding RNA homology searches) Washington (USA)
- RAxML-VI-HPC (maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models) Lausanne (Suisse)
- Recco (recombination analysis using cost optimization) Max-Planck (Allemagne)
- ReDiT (Repeat Discrepancy Tagger - A Shotgun Assembly Finishing Aid) Stockholm (Suède)
- RCGScanner (analysis of regulon structures in different bacterial genomes) Barcelone (Espagne)
- RDP2 (recombination detection and analysis from sequence alignments) Vigo (Espagne)
- RED-T (utilizes the Ratio of Evolutionary Distances for determination of alternative phylogenetic events) Georgia (USA)
- REGA (HIV-1 Subtyping Tool) Oxford (UK)
- Regression trees for regulatory element identification Daejeon (Corée)
- Repseek (a tool to retrieve approximate repeats from large DNA sequences) Jussieu (France)
- Rfold (an exact algorithm for computing local base pairing probabilities) Tokyo (Japon)
- rh_tsp_map 3.0 (end-to-end radiation hybrid mapping with improved speed and quality control) NCBI (USA)
- RHOM (Research of HOMogeneous regions in DNA sequences) INRA (France)
- Ribostral (an RNA 3D alignment analyzer and viewer based on basepair isostericities) BGSU (USA)
- RNA db tools BiRC (Danemark)
- RNALI (analyzes rRNA sequence) PBIL (France)
- RNA folding, modeling and secondary structure display RPI (Zuker)
- RNAGA (Prediction of common secondary structures of RNAs by genetic algorithm) NCI (USA)
- RNAmicro (recognizing microRNA precursors in comparative genomics data) Leipzig (Allemagne)
- RNAML (syntax for exchanging RNA information) Montreal (Canada)
- RNAMOT, ISOPAIR ESIL (France)
- RNAshapes (an integrated RNA analysis package based on abstract shapes) Bielefeld (Allemagne)
- R Package (Multidimensional analysis, spatial analysis) Montreal (Canada)
- RPMs (the newly released NCBI Blast and clustalw-1.81 code) Scalable Informatics
- R/qtlbim (QTL with Bayesian Interval Mapping in experimental crosses) Madison (USA)
- rRNA Software (Ranfold, TreeCon) Antwerp (Belgique), voir aussi RnaViz
- RRTree (relative-Rate Tests with a tree) PBIL (France)
- S2S (display, manipulate and interconnect RNA data from sequence to structure) Strasbourg (France)
- SALTO (a structure-based method for protein sequence alignment) NCBI (USA)
- SARMENT (python modules for HMM analysis and partitioning of sequences) PBIL (France)
- SATCHMO (sequence alignment and tree construction using hidden Markov models) California (USA)
- SAM (Sequence Alignment and Modeling System) www
- SAT (sequence search algorithm assessment and testing toolkit) MRC-LMB (UK)
- SatDNA Analyzer (a computing tool for satellite-DNA evolutionary analysis) Granada (Espagne)
- Saturated BLAST La Jolla (USA)
- SBML ODE Solver Library (a native API for symbolic and fast numerical analysis of reaction networks) Vienne (Autriche)
- SCI Software (SCIrun, Map3d, BioPSE, Unintah, VISPack) UTAH (USA)
- SCOOP (a simple method for identification of novel protein superfamily relationships) Sanger (UK)
- SCRM (learning probabilistic models of cis-regulatory modules that represent logical and spatial aspects) Wisconsin (USA)
- SeaView (graphical multiple sequence alignment editor) PBIL (France)
- SEALS (A System for Easy Analysis of Lots of Sequences) NCBI (USA)
- SEAN (SNP prediction and display program utilizing EST sequence clusters) Londres (UK)
- SELFID (Self-identification of coding regions in microbial genomes) IGS (France)
- SEPON (a selection and evaluation pipeline for oligonucleotides) Tjele (Danemark)
- seq++ (analyzing biological sequences with a range of Markov-related models) Evry (France)
- SeqHound Blueprint
- SEQIO
ftp.cs.ucdavis.edu under pub/strings/, documentation Pasteur
- SequenceLDhot (detecting recombination hotspots) Lancaster (UK)
- Sequencing Software Sanger (UK)
- SEQREP1 (representation of DNA sequences with virtual potentials and their processing by (SEQREP) Kohonen self-organizing maps) Lisbone (Portugal)
- SeqVISTA (Graphical Tool for Sequence Feature Visualization and Comparison) Boston (USA)
- Serial SimCoal (a population genetics model for data from multiple populations and points in time) Stanford (USA)
- sGAL (a computational method for finding surface exposed sites in proteins suitable for Cys-mediated cross-linking) Toronto (Canada)
- SGN Sim (a Stochastic Genetic Networks Simulator) Calgary (Canada)
- SIG (automated generation and refinement of protein signatures) Leeds (UK)
- SIM4 (to align cDNA and genomic DNA) Pennsylvania (USA)
- SimiTri (visualizing similarity relationships for groups of sequences) Nematodes
- simuPOP (a forward-time population genetics simulation environment) Houston (USA)
- siRNA (gene specific siRNA selector) Philadelphia (USA)
- SISSI (simulating sequence evolution with site-specific interactions) Dusseldorf (Allemagne)
- SITEBLAST (rapid and sensitive local alignment of genomic sequences employing motif anchors) Max Planck (Allemagne)
- SlidingBayes (exploring recombination using a sliding window approach based on Bayesian phylogenetic inference) Leuven (Belgique)
- Sliding MinPD (building evolutionary networks of serial samples via an automated recombination detection approach) Miami (USA)
- SMILE (tool that infers motifs in a set of sequences) IGM (France)
- 2SNP (scalable phasing based on 2-SNP haplotypes) Atlanta (USA)
- SNP4 linkage (identification of linked regions using high-density SNP genotype data in linkage analysis) Kowloon (Hong-Kong)
- SNAP (combine and map modules for multilocus population genetic analysis) North Carolina (USA)
- SNPLINK (multipoint linkage analysis of densely distributed SNP data incorporating automated linkage disequilibrium removal) Surrey (UK)
- SNPNB (analyzing neighboring-nucleotide biases on single nucleotide polymorphisms) Richmond (USA)
- SNPP (automating large-scale SNP genotype data management) Hunan (Chine)
- SOAP (cleaning multiple alignments from unstable blocks) IMBM (Belgique)
- SOAP-based Analysis Web Service EBI (EBI)
- Software at Caltech (USA)
- Software (pip, mb-coda, ABaCUS,..) at CARB (USA)
- Software (Glad, Manor, Maia, ProMS, CapWeb, Vamp) at Institut Curie Bioinformatics Unit Curie (France)
- Software (Arachne, Argo, Haploview , LocusView, Sweep, Tagger, GeneHunter, MapMaker, GenePattern, GSEA, GeneCruiser, Primer3, RHMapper) MIT (USA)
- Software (BiopSe, Map3D) at NCRR (USA)
- Software (Phylogenetic analysis, Ancestral sequences, Phylogenetic test of adaptive evolution, Population trees from genetic markers, Heterozygosities and Gst...) Pennstate (USA)
- Software (QTree, ProFit, MINT, NW, Torsions, AVP, Apat) at RUBiC
- Software at Sanger Centre Sanger (UK)
- Software (Stem-loop detector, BLOSpectrum, SMaRTFinder, Suffix Trees, Protein Folding in CLP(FD), Modified Sputnik) Udine (Italie)
- Software (Chasalow, ComBin, Crooschecker, CPSIM, CGT, Peditree, Kweker, MQA, MapInspect, PhylTools, Record, Precise, Splitloc, BCSIM) Wageningen (Netherlands)
- Software at WashU (Hmmer, Pfam, Atv, Cove, Forester, Infernal, TrnaScan, Recon, RnaBob, Suqid, Qrna, PkNots, NCRNASCAN, HMMERVIEWER) Washington (USA)
- Software at Department of Genetics (Consensus, Patser, Landscape, GenParser, PromFD, Co-Bind, PhyloCon, comRNA) Washington (USA)
- Software for Biology (PC) ANNHYB (France)
- Software for genetics analysis (Structure, TreeLD, Strat, MaldSoft) Chicago (USA)
- Software for structure determination and analysis PDB (USA)
- Software from the Computational Molecular Biology Group (FootPrinter, YMF, Slam, Phyme, Cosmo, Projection, Dapple) Washington (USA)
- Software from the Department of Human Genetics (APM, FastSLINK, MEGA2, Pedcheck, Simibd,..) Pittsburgh (USA)
- Software tools for EST analysis (RBR, Cluster, xsact, xtract) Bergen (Norvège)
- SOLAR (Sequential Oligogenic Linkage Analysis Routines) SFBR
- SOMBRERO (finds regulatory elements in a set of DNA sequences) Galway (Irlande)
- SPACER (identification of cis-regulatory elements with non-contiguous critical residues) Hanover (USA)
- SparseLOGREG (simple and efficient algorithm for gene selection using sparse logistic regression) Singapore
- SPEL (prediction of functional specificity determinants from protein sequences using log-likelihood ratios) Texas (USA)
- SPLASH (Structural pattern localization analysis by sequential histogram) IBM (USA)
- SPST (modeling the sparse nature of protein sequences) Sao Paolo (Brésil)
- Sputnik (searches dna sequence for microsatellite repeats) Abajian (USA)
- SQUINT (a multiple alignment program and editor) Auckland (Nouvelle-Zélande)
- SSAHA (tool for very fast matching and alignment of DNA sequences) Sanger (UK)
- S-SPatt (simple statistics for patterns on Markov chains) Evry (France)
- S-system (parameter estimation using Simulated Annealing for S-system models of biochemical networks) Munich (Allemagne)
- SSAKE (assembling millions of short DNA sequences) Vancouver (Canada)
- SSGS (a permissive secondary structure-guided superposition tool for clustering of protein fragments toward protein structure prediction via fragment assembly) Tel Aviv (Israel)
- Staden Package open source project
- STAR (folding of RNA) Leiden (The Netherlands)
- Statistiques des séquences (R'MES, R'PRO...) INRA (France)
- StochSim (a stochastic simulator for chemical reactions) Cambridge (UK)
- STOCKS (STOChastic Kinetic Simulation of biochemical processes with Gillespie algorithm) Warszawa (Pologne)
- Stormo Laboratory software (Consensus, Landscape, GenParser, PromFD, Co-Bind, Co-Bind, PhyloCon) St Louis (USA)
- STRAL (progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time) Dusseldorf (Allemagne)
- STROLL (a Fragment Assembly Program for Large-Scale Genome Sequencing) Harvard
- SURFNET v.1.4 (generates surfaces and void regions between surfaces) UCL (UK)
- Swissknife (Perl library to handle entries in SWISS-PROT format) EBI (UK)
- SWISS-PdbViewer (Macintosh) Expasy
- SYMMETREE (whole-tree analysis of differential diversification rates) Yale (USA)
- SynBrowse (a synteny browser for comparative sequence analysis) Iowa (USA)
- Systems Biology Software at the Keck Graduate Institute Keck (USA)
- Table View (a generalized scientific visualization program for exploration of various biological data, including EST, SAGE, microarray and annotation) Minnesota (USA)
- TAGster (efficient selection of LD tag SNPs in single or multiple populations) NIH (USA)
- TAMO (a flexible, object-oriented framework for analyzing transcriptional regulation using DNA-sequence motifs) Cambridge (USA)
- Tandem repeats New York (USA)
- TandTRAQ (an open-source tool for integrated protein identification and quantitation) Oregon (USA)
- Target Finder (software for antisense oligonucleotide target site selection based on MAST and secondary structures of target mRNA) Beijing (Chine)
- TASSEL (software for association mapping of complex traits in diverse samples) Cornell (USA)
- Taxonomic Markup Language (XML) Albany (USA)
- TBRM (enabling high-throughput data management for systems biology: The Bioinformatics Resource Manager) Richland (USA)
- TFBS (identification based on genetic algorithm with combined representations and adaptive post-processing) Hong-Kong
- TBSFinder (a method for identifying transcription factor binding sites in yeast) Taipei (Taiwan)
- T-COFFEE (Multiple Alignments) IGS (France)
- TESD (a transposable element dynamics simulation environment) PBIL (France)
- T-REX (Tree and reticulogram Reconstruction) Montréal (Canada)
- Terminus (telomeric end-read mining in unassembled sequences) Kentucky (USA)
- TFBS (Perl modules for transcription factor detection and analysis) Stockholm (Suède)
- THESEUS (maximum likelihood superpositioning and analysis of macromolecular structures) Colorado (USA)
- THESIAS (testing haplotype effects in association studies) Paris VI (France)
- THREADER (predicting protein tertiary structure by recognizing the correct fold from a library of alternatives) Version 3.5 (UK)
- TIGR Software Tool Collection (MIDAS, MADAM, MEV, Spotfinder, HMMsearch, Panda, Genomic Assembly, Mummer, AMOS, BAMBUS, AutoEditor, Assembler, Lucy, MUMmer, AAT package, DAGchainer, MANATEE, PIRATE, PASA, GlimmerHMM...) TIGR (USA)
- TIGR Gene Indices Software Tools (Clustering, clview, SeqClean, cdbfasta/cdbyank, DAS/XML) TIGR (USA)
- TimeClust (a clustering tool for gene expression time series) Pavie (Italie)
- TINKER St. Louis (Molecular Modeling Package), distribution aussi de PROPAK, SLEUTH, QSAR, GETPDB
- TIP (protein backtranslation aided by genetic algorithms) Santiago (Chili)
- Titri (Enzyme Linked Immuno Assay calculations) Vidarsson
- ToolDiag (pattern recognition toolbox) UFES (Brésil)
- TOPD/FMTS (a new software to compare phylogenetic trees) Tarragona (Espagne)
- TOPP (the OpenMS proteomics pipeline) Tubingen (Allemagne)
- TOPAL (detecting mosaic sequences and rate heterogeneity in phylogenetic datasets) BioSS (UK)
- TopoICE-R (3D visualization modeling the topology of DNA recombination) Iowa (USA), autre lien
- TRA (software program combining sequence motif searches with keywords for finding repeats containing DNA sequences) Antalya (Turquie)
- TraceEdit (a DNA trace editor and viewer) Wurzburg (Allemagne)
- Transterm (rho-independent transcription terminators in bacterial genomes) Maryland (USA)
- TRAP (predicting transcription factor affinities to DNA from a biophysical model) Berlin (Allemagne)
- TREBLE (tree and rate estimation by local evaluation of heterochronous nucleotide data) California (USA)
- Treefinder (phylogenetic trees from nucleotide sequences) Gangolf (Allemagne)
- TreeJuxtaposer(Scalable Tree Comparison using Focus+Context with Guaranteed Visibility) Columbia (Canada)
- Tree-Puzzle (Maximum likelihood analysis for nucleotide, amino acid, and two-state data) Leipzig (Allemagne)
- TreeQ-VISTA (an interactive tree visualization tool with functional annotation query capabilities) California (USA)
- TreeSnatcher (coding trees from images) Vienne (Autriche)
- TreeView X Glasgow (UK)
- TRFMA (a web-based tool for terminal restriction fragment length polymorphism analysis based on molecular weight) Fukuoka (Japon)
- TribeMCL (method for clustering proteins into related groups) EBI (UK)
- TRNinfer (inferring transcriptional regulatory networks from high-throughput data) Osaka (Japon)
- TruMatch (a BLAST post-processor that identifies bona fide sequence matches to genome assemblies) Kentucky (USA)
- TSS Prediction (improved prediction of bacterial transcription start sites) Queensland (Australie)
- TUNA (association studies for untyped markers) Chicago (USA)
- TU predictor (using functional and organizational information to improve genome-wide computational prediction of transcription units on pathway-genome databases) BioCyc (USA)
- TWAIN (efficient implementation of a generalized pair hidden Markov model for comparative gene finding) TIGR (USA)
- TWINSCAN/N-SCAN (gene-prediction system) Washington (USA)
- Two Sample Logo (a graphical representation of the differences between two sets of sequence alignments) Indiana (USA)
- UCSF Public Resources (Protein Modeling) Fred Cohen Laboratory (USA)
- UniMarker (UM) method for synteny mapping of large genomes Taipei (Taiwan)
- UREC (inferring phylogeny from whole genomes) Varsovie (Pologne)
- Unrooted (tree drawing program) PBIL (France)
- USC Computational Biology Software Packages (Alignment, Chimera, DNA spectrum, Procrustes,..) USC (USA)
- USF software (Macromolecular Crystallography and Structural Biology) Uppsala (Suède)
- VariScan (analysis of evolutionary patterns from large-scale DNA sequence polymorphism data) Barcelone (Espagne)
- VEIL (hidden Markov model for finding genes in vertebrate DNA) TIGR (USA)
- VEMS (interpreting peptide mass spectra) Aalborg (Danemark)
- VigyaanCD (Linux-live CD containing all the required software to boot the computer with ready to use chemistry, biology tools) ORNL (USA)
- Vienna RNA Package Vienna (Autriche)
- VisBio (biological visualization tool designed to allow easy visualization and analysis of 4-D multispectral data) Wisconsin (USA)
- VISSA (a program to visualize structural features from structure sequence alignment) La Jolla (USA)
- VISTA (VISualization Tool for Alignments) LBL (USA)
- ViTO (a tool for homology modelling and protein family study) Montpellier (France)
- VizRank (finding informative data projections in functional genomics by machine learning) Ljubljana (Slovénie)
- VMD (visual molecular dynamics) Illinois (USA)
- Voro3D (3D Voronoi tessellations applied to protein structures) Jussieu (France)
- W2H (WWW Interface to the GCG Sequence Analysis Software Tools) EBI
- Watson (statistical test to detect genetic divergence among populations from DNA fingerprinting data) Pavie (Italie)
- WCLUSTAG (combining functional and linkage disequilibrium information in the selection of tag SNPs) Hong Kong
- Webace (set of CGI scripts and perl modules to enable acedb databases to be accessed via WWW) Sanger (UK)
- WebinTool (generic WWW to SQL-database interface) Roslin (UK)
- WebMol II (Java-based 3D viewer for protein structuresJava-based 3D viewer for protein structures) Stanford (USA)
- WebMOTIFS (automated discovery, filtering and scoring of DNA sequence motifs using multiple programs and Bayesian approaches) MIT (USA)
- Web Services (WSDbfetch, WSFasta, WSWUBlast, WSInterProScan, SoapLab, MSD Services) EBI (UK)
- WEKA (data mining in bioinformatics) Hamilton (Nouvelle Zélande)
- wEMBOSS (a web interface for EMBOSS) La Plata (Argentine)
- WGLRH (a whole genome long-range haplotype test for detecting imprints of positive selection in human populations) Santa Clara (USA)
- WHAP (haplotype-based association analysis) Cambridge (USA)
- WinQtlCart (mapping quantitative trait loci) NCSU (USA)
- Wordom (a program for efficient analysis of molecular dynamics simulations) Zurich (Suisse)
- Wrapping up BLAST and other applications for use on Unix clusters Dublin (Irlande)
- XAct (maintain and record the results of crystallisation experiments) Aarhus (Danemark)
- xlSTAT www
- XmMol (macromolecular visualization with X11) Jussieu (France)
- XML for Molecular Biology CBR (Canada)
- XML Spec NCBI (USA)
- XNBC (package for simulating biological neural networks) Jussieu (France)
- YASS (local alignment of DNA sequences) LIFL (France)
- Zerg (a very fast BLAST parser library written in C) Sao Paulo (Brésil)
- ZFIQ (a software package for zebrafish biology) China
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