Databases and Analysis tools by ftp
English version of ABIM : Banques et logiciels disponibles par ftp
Databases
- Major sites
- Specialized sites
Software
- Catalogs
- Major sites
- EBI :
ftp.ebi.ac.uk (Unix, VMS, Mac, PC) Bio Catalog, mirror at 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, see also 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
- Specialized sites or out of 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, see also acedb
- AClAP (autonomous hierarchical agglomerative cluster analysis based protocol to partition conformational datasets) Bologna (Italy)
- 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 (French)
- ADP_EM (fast exhaustive multi-resolution docking for high-throughput coverage) Madrid (Spain)
- 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 (Germany)
- 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 (Germany)
- ALGGEN (Algorithmics and Genetics : Dotlet) Barcelona (Spain)
- ALIDOT (Detecting Conserved RNA Structures) Wien (Austria)
- Alien_hunter (interpolated variable order motifs for identification of horizontally acquired DNA) Sanger (UK)
- Align-m (multiple alignment of highly divergent sequences) Brussel (Belgium)
- AlignACE Harvard (USA)
- Alignment Editors SeaView (France)
- ALOHOMORA (a tool for linkage analysis using 10K SNP array data) Berlin-Buch (Germany)
- AlphaSimp (Simplifying amino acid alphabets by means of a branch and bound algorithm and substitution matrices) CRIBI (Italy)
- 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 (Australia)
- 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 (French)
- APAT (an extensible automated protein annotation tool: standardizing input and output using validated XML) London (UK)
- Apollo (Drosophila Genome Browser) BDGP
- ARB (A Software Environment for Sequence Data) Max-Planck, see also (Germany)
- ARCS (an aggregated related column scoring scheme for aligned sequences) Cleveland (USA)
- ARLEQUIN (population genetic data analysis) Geneva (Switzerland)
- ARTEMIS (DNA sequence viewer and annotation tool) Sanger (UK)
- Molecular Assembly Sequence Software (Macintosh) Carol
- ASPEX Package (Affected Sib Pair Exclusion Mapping) Stanford (USA)
- ATR (exhaustive whole-genome tandem repeats search) Singapore
- 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 (Germany)
- BADASP (predicting functional specificity in protein families using ancestral sequences) Dublin (Ireland)
- BAli-Phy (simultaneous Bayesian inference of alignment and phylogeny) UCLA (USA)
- BALLView (a tool for research and education in molecular modeling) Saarbrucken (Germany)
- BAPS 2 (enhanced possibilities for the analysis of genetic population structure) Helsinki (Finland)
- 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 (Switzerland)
- 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 (French)
- Bioconductor (open source for the analysis and comprehension of genomic data) bioconductor
- BIODEV (MatInd, ConsInspector, CoreSearch, GenomeInspector, FastM, Model generator, DIALIGN) BIODEV (Germany)
- 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 (French)
- Biology Debian package Pasteur (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 (French)
- 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 : Germany), see also BioPerl, see also 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 (Poland)
- BioSVG (Perl framework to generate Scalable Vector Graphics) CCMB (India)
- BioTEX (LaTex2 bio extensions) Tuebingen (Germany)
- BioWidgets Consortium (Graphical displays of genome data) Berkeley (USA)
- BioWidgets for Java CBIL (USA)
- Biskit (a software platform for structural bioinformatics) Pasteur (French)
- 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 (Ireland)
- Blast (longer words for protein seeding) NCBI (USA)
- Blixem (a graphical blast viewer) Karolinska (Sweden)
- BMapBuilder (building chromosome-wide LD maps) Granada (Spain)
- BNetDyn (stochastic boolean network dynamics ) SIB (Switzerland)
- BRAGI (protein modelling and display program) GBF (Germany)
- 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 (Japan)
- 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 (India)
- CAPS (coevolution analysis using protein sequences) Dublin (Ireland)
- CARNAC (Computer Alignment of RNA by Cofolding) LIFL (French)
- CarthaGene (multipopulation integrated genetic and radiation hybrid mapping) INRA (French)
- 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) Sevilla (Spain)
- 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), see alos 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 (Hungary)
- ChemWeb (to draw chemical structures) SoftShell (USA)
- Chime Resources Massachusetts (USA), see also 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 (China)
- CisPlusFinder (identifying cis-regulatory modules by combining comparative and compositional analysis of DNA) Cologne (Germany)
- CITA (programming interface that allows access to one or more ACEDB databases through CORBA) JIC (UK)
- Clann (investigating phylogenetic information through supertree analyses) Kildare (Ireland)
- ClassMaker (electrophoretic data classification for phylogenetics and biostatistics) Perugia (Italy)
- Clearcut (a fast implementation of relaxed neighbor joining) Moscow (Russia)
- Cleaver (software for identifying taxon specific restriction endonuclease recognition sites) Kingston (Australia)
- 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 with graphical interface : 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 (Austria)
- 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)
- ColorHOR (graphical algorithm for fast scan of alpha satellite higher-order repeats) Zagreb (Croatia)
- ComAlign (Combining many multiple alignments in one improved alignment) Aarhus (Denmark)
- Co-Bind, Landscape, GenParser, Consensus Washington (USA)
- 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 (French)
- COMPAM (visualization of combining pairwise alignments for multiple genomes) Indiana (USA)
- Compressed suffix tree-a basis for genome-scale sequence analysis Helsinki (Finland)
- COMPUCELL (a multi-model framework for simulation of morphogenesis) Missouri (USA)
- Computational Biology Group - DAIMI (ComAlign, CombAt, HMMComp, Hudson, RecPars, StatAl, Qdist ...) Aarhus (Denmark)
- 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 (Japan)
- ConStruct (prediction of conserved secondary structure of a set of homologous single-stranded RNA) Duesseldorf (Germany)
- COPASI (a COmplex PAthway SImulator) Blacksburg (USA)
- COPYCAT (cophylogenetic analysis tool) Tübingen (Germany)
- CORBA-Java based Application Wrapper EBI (UK)
- CpGProD (CpG Island Promoter Detection) PBIL (French)
- CRANN (detecting adaptive evolution in protein-coding DNA sequences) Maynooth (Ireland)
- CREx (inferring genomic rearrangements based on common intervals) Leipzig (Germany)
- CSPro (identification and visualization of cage-shaped proteins) Hangzhou (China)
- CS-PSeq-Gen (Simulation of protein sequences under constraints) Jussieu (French)
- CTree (analysis of clusters on phylogenetic trees) Manchester (UK)
- Cyclone (java-based querying and computing with Pathway/Genome databases) Evry (French)
- CyDAS (a cytogenetic data analysis system) Marburg (Germany)
- Cyto-Sim (a formal language model and stochastic simulator of membrane-enclosed biochemical processes) Catanzaro (Italy)
- DaliLite (pairwise structure comparison and database searching) EBI
- DAMBE (Data Analysis in Molecular Biology and Evolution) Ottawa (Canada)
- Darwin CBRG (Switzerland)
- DASS (efficient discovery and p-value calculation of substructures in unordered data) Jena (Germany)
- 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 (French)
- DGSplicer (prediction of splice sites with dependency graphs and their expanded bayesian networks) Hsinchu (Taiwan)
- DICOPROT (DICHROism of PROTeins) IBCP (French)
- DINO (Visualizing Structural Biology) Biozentrum (Switzerland)
- DISCAS (characterization of chemical carcinogens studied by the cascade model) Nishinomiya (Japan)
- DIVCLUS (protein sequence domain clustering program) MRC (UK)
- Dizzy (a method for estimating stochastic noise in large genetic regulatory networks) Seattle (USA)
- 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 Barcelona (Spain)
- DOCK (Molecular docking simulations) UCSF (USA)
- Domain Finder (characterization of dynamical domains in proteins) Orléans (French)
- Dotter (a dot-matrix program with interactive greyscale rendering for genomic DNA and Protein sequence analysis) Karolinska (Sweden)
- 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 (Germany)
- 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)
- 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 (Germany)
- ERPIN (Easy RNA Profile IdentificatioN) TAGC (French)
- ESPript (multiple sequence alignments in PostScript) IBCP (French)
- ESSA (RNA secondary structure analysis) INRA (France)
- ESTAP (an automated system for the analysis of EST data) Virginia (USA)
- ESTate (Expressed Sequence Tag Analysis Tools) EBI (UK)
- EST analysis tools Bergen (Norway)
- 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)
- ESTprep (preprocessing cDNA sequence reads) Iowa (USA)
- ESTWeb (software package designed for uniform data processing and storage for large-scale EST sequencing projects) Sao Paulo (Brasil)
- 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 (Germany)
- Fast and accurate database homology search using upper bounds of local alignment scores Kyoto (Japan)
- 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 (New Zealand)
- Flow Cytometry www (Salk)
- FoldAlign (pairwise local structural alignment of RNA sequences with sequence similarity less than 40%) Frederiksberg (Denmark)
- Folding@home (simulates protein folding ("distributed dynamics")) Stanford (USA)
- Forage (SNP discovery using advanced algorithms and neural networks) Stockholm (Sweden)
- 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 (French)
- 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 (Spain)
- 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 (Croatia)
- GASP (Genometric analysis simulation program) NHGRI-NIH (USA)
- GCUA (General Codon Usage Analysis) Maynooth (Ireland)
- 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 (South Africa)
- GEANFAMMER (GEnome ANalysis and Protein FAMily MakER) MRC (UK)
- GEAR (genomic enrichment analysis of regional DNA copy number changes) Seoul (Korea)
- Gemoda (a generic motif discovery algorithm for sequential data) MIT (USA)
- GENDB (open source genome annotation system) Bielefeld (Germany)
- 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 (Germany)
- 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 (
- GeneSyn (tool for detecting conserved gene order across genomes) Milano (Italy)
- 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 (Japan)
- GenoExpertBacteria (exploration of bacterial genomic, proteic and functional data) INRIA (French)
- 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 (French)
- Gepard (a rapid and sensitive tool for creating dotplots on genome scale) Neuherberg (Germany)
- Gepasi (Biochemical simulation) Aberystwyth (Wales)
- GFF: an exchange format for gene-finding Sanger (UK)
- GFFtools (gff2ps, gff2aplot) Pompeu Fabra (Spain)
- Ghemical (computational chemistry software package released under the GNU GPL) Kuopio (Finland)
- GINsim (dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle) Marseille (French)
- 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 (French)
- GOAT (Genome Organization Analysis Tool) Virginia (USA)
- GOLD (Graphical Overview of Linkage Disequilibrium) Oxford (UK)
- GPRIME (PCR primers tools) ANU (Australia)
- GRAMM (program for protein docking) Kansas (USA)
- Grappe (fast searching a text file for regular expressions) Loria (French)
- GRASP (Graphical Representation and Analysis of Structural Properties) Columbia (USA)
- GRAST (a new way of genome reduction analysis using comparative genomics) Maynooth (Ireland)
- 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 (Germany)
- 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 (Germany)
- HMM (PASSML and PASSML-TM) EBI (UK)
- HMMCOMP (Comparison of hidden Markov models) Aarhus (Denmark)
- 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 (Belgium)
- ICM-Browser (structural biology) MolSoft
- Imagene Notebook (cooperative computer environment for the annotation and analysis of genomic sequences) Jussieu (French)
- IMEx (Imperfect Microsatellite Extractor) Hyderabad (India)
- IML (prediction of RNA Secondary Structures with Pseudoknots) Washington (USA)
- IMP services (GPI predictor, SSCP, NSC,..) IMP (Austria)
- INCA (synonymous codon usage analysis and clustering by means of self-organizing map) Zagreb (Croatia)
- 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 (Germany)
- Ingenenue (Genetic Network Construction Software) NSF (USA)
- IntegraGen (open source package for molecular biology) urbigene
- Intergenic sequence inspector (searching and identifying bacterial RNAs) Rennes (French)
- InterProScan Package EBI (UK), see also
- 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 (Korea)
- IRILmap (linkage map distance conversion software for intermated recombinant inbred lines) INRA (French)
- 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 (French)
- 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 (Germany)
- 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 (Germany)
- KGML-ED (dynamic exploration and editing of KEGG pathway diagrams) Gatersleben (Germany)
- KGraph (a system for visualizing and evaluating complex genetic associations) Michigan (USA)
- Kinetikit (adaptive stochastic-deterministic chemical kinetic simulations) Bangalore (India)
- KtreeDist (quantification of differences in the relative branch length and topology of phylogenetic trees) Barcelona (Spain)
- LDAba (java-based linkage disequilibrium analyzer) CAMS (China)
- LDDist (Perl module for calculating LogDet pair-wise distances for protein and nucleotide sequences) Uppsala (Sweden)
- 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 (Turkey)
- 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)
- 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 (China)
- 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, see also 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 (Japan)
- MAGPIE (Automated Genome Project Investigation Environment) Rockfeller (USA), see alos Calgary (Canada)
- Make2D-DB II Package (to create, convert, interconnect and keep up-to-date 2-DE databases) Expasy (Switzerland)
- 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 (Belgium)
- Mapper Illinois (USA)
- 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)
- Maptools (programs for working with experimental three-dimensional (density) maps) Gottingen (Germany)
- 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 (French), see also PolyXmass
- MASTR (multiple alignment and structure prediction of non-coding RNAs using simulated annealing) Copenhagen (Denmark)
- MatCompare (methods for comparing transcription factor binding site (TFBS) position frequency matrices (PFMs)) CSHL (USA)
- MatInd and MatInspector, ConsInd and ConsInspector, GeneInspector etc. BIODV (to derive a matrix description of a consensus and to detect consensus matches in nucleotide sequence data, ORF ..) (Germany)
- 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 (Japan)
- McClellan Lab Software (TreeSAAP, DataConvert, CDM, CDSParser, AlignmentHelper, SimSeq) BYU (USA)
- MCMCSALUT (Markov Chain Monte Carlo Sequence Alignment Utility) Frankfurt (Germany)
- MC-SYM (Nucleic acids 3D-structure prediction) MC-SYM (Canada)
- MCell (A General Monte Carlo Simulator of Cellular Microphysiology) Salk Institute (USA), another link
- Mclip (motif detection based on cliques of gapped local profile-to-profile alignments) Canberra (Australia)
- MED-Start (for identifying translation initiation sites in microbial genomes) Nanjing (China)
- MEGA (Molecular Evolutioary Genetics Analysis) Megasoftware
- MEMSAT (prediction of the secondary structure and topology of all-helix integral membrane) UCL (PC only) (UK)
- Metabolic Control Analysis (Scamp, Metacon, Empath, Metatool) Oxford (UK)
- Metabolic tools (METATOOL, BlockDiag, OptiMode, Separator) Jena (Germany)
- 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 (Germany)
- 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 (Italy)
- AffyR (package to use oligonucleotide microarrays data) CBS (Denmark)
- AGScan (a pluggable microarray image quantification software based on the ImageJ library) INRA (French)
- 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 (Japan)
- ArrayDB Software NHGRI (USA)
- ArrayExpress Software EBI (UK)
- BagBoosting (for Tumor Classification with Gene Expression Data) Zurich (Switzerland)
- Base (manage the massive amounts of data generated by microarray analysis) Lund (Sweden)
- BGX (flexible Bayesian clustering and partition models for gene expression data) London (UK)
- Bioconductor Harvard (USA), see also Bioconductor Packages
- BNArray (an R package for constructing gene regulatory networks from microarray data by using Bayesian network) Hangzhou (China)
- Boosting for tumor classification with gene expression data ETHZ (Switzerland)
- 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 (Australia)
- Clusterv (a tool for assessing the reliability of clusters discovered in DNA microarray data - R package) Milano (Italy)
- CoCo (a web application to display, store and curate ChIP-on-chip data integrated with diverse types of gene expression data) Heidelberg (Germany)
- 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 (French)
- Dual-genome (primer design for construction of DNA microarrays) Stockholm (Sweden)
- EDGE (extraction and analysis of differential gene expression) Washington (USA)
- eQTL Explorer (integrated mining of combined genetic linkage and expression experiments) London (UK)
- FARMS (R package for Factor Analysis for Robust Microarray Summarization) Linz (Austria)
- 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) Milano (Italy)
- GandrKB (ontological microarray annotation and visualization) Berlin (Germany)
- GARBAN (genomic analysis and rapid biological annotation of cDNA microarray and proteomic data) Pamplona (Spain)
- 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 (French)
- 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 (Germany)
- IGG (tool to integrate GeneChips for genetic studies) Hong Kong (China)
- I/NI-calls (for the exclusion of non-informative genes: a highly effective filtering tool for microarray data / R-package) Linz (Austria)
- 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 (French)
- limmaGUI (a graphical user interface for linear modeling of microarray data) Parkville (Australia)
- LAP (to identify differentially expressed chromosomal regions) Padua (Italy)
- Libaffy (software for processing Affymetrix(R) GeneChip(R) data) South Florida (USA)
- Machaon (an integrated tool for microarray data clustering and cluster validity assessment) Dublin (Ireland)
- MACGT (multi-dimensional automated clustering genotyping tool for analysis of microarray-based mini-sequencing data) Vancouver (Canada)
- MADGE (scalable distributed data management software for cDNA microarrays) Florida (USA)
- Magic Tools (integrated microarray data analysis) Davidson (USA)
- Max Planck (Germany) (MACAT, Stam, compdiagTools)
- MAIA (package for automatic microarray image analysis) Institut Curie (French)
- maSigPro (a method to identify significantly differential expression profiles in time-course microarray experiments) Valencia (Spain)
- MASQOT-GUI (spot quality assessment for the two-channel microarray platform) Umea (Sweden)
- 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 (Germany)
- Microarray data mining with visual programming Ljubljana (Slovenia)
- 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 (Denmark)
- OLIN (optimized normalization, visualization and quality testing of two-channel microarray data) Berlin (Germany)
- 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 (Germany)
- 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 (Turkey)
- Plato (robust cluster analysis of microarray gene expression data) Georgia (USA)
- ProMAT (protein microarray analysis tool) Richland (USA)
- Quantum clustering (Mathlab) Tel Aviv (Israel)
- Rosetta (learning rule-based models of biological process from gene expression time profiles using Gene Ontology) Trondheim (Norway)
- R code for the empirical Bayes Madison (USA)
- R package (Statistics for Microarray Analysis) Berkeley
- R-Web Glasgow (UK)
- YASMA Birbeck
- Rosetta (learning rule-based models of biological process from gene expression time profiles using Gene Ontology) Trondheim (Norway)
- R Packages For Gene Expression Analysis (links) Munchen
- 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 (Denmark)
- TAPPA (topological analysis of pathway phenotype association) Wisconsin (USA)
- THEA (ontology-driven analysis of microarray data) Nice (French)
- 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 (French)
- 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 (French)
- MMTSB software (Modelling package, Charm, Tool set, Yammp) SRI (USA)
- Möbius (an integrated discrete-event modeling environment) Illinois (USA)
- Modelisation (genetic et molecular) : (R'MES, R'PRO, SliceEMBL, SeqFold) SSB (French)
- 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 (Sweden)
- 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 (The Netherlands)
- 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 (French)
- Molekel (molecular visualization package) CSCH (Switzerland)
- MolFit (protein-protein docking) Rehovot (Israel)
- MolMol (MOLecule analysis and MOLecule display) ETHZ (Switzerland)
- MOLPHY (Computer Program Package for Molecular Phylogenetics) Tokyo (Japan)
- Molscript Avatar
- Moma (analysis of optimality in natural and perturbed metabolic networks) Harvard (USA)
- MotifRank (computing exact P-values for DNA motifs) Beijing (China)
- MPEx (Membrane Protein Explorer) Irvine (USA)
- mpiBLAST (open source parallelization of NCBI BLAST) LANL (USA)
- MPSA (Multiple Protein Sequence Analysis) PBIL (French)
- MrBayes (Bayesian inference of phylogeny) Florida (USA)
- MREPS (finding tandem repeats) IFL (French)
- 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 (Germany)
- MSS (whole genome alignment using a mutation sensitive approach) Hong Kong (China)
- 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 (Germany)
- MuGeN (simultaneous exploration of multiple genomes and computer analysis results) INRA (French)
- MulBlast (gathering BLAST pairwise alignments in one multiple alignment) Montpellier (French)
- MultiParanoid (automatic clustering of orthologs and inparalogs shared by multiple proteomes) Stockholm (Sweden)
- MultiPLX (automatic grouping and evaluation of PCR primers) Tartu (Estonia)
- 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) Copenhagen (Denmark)
- 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) Milano (Italy)
- MZmine (toolbox for processing and visualization of mass spectrometry based molecular profile data) Espoo (Finland)
- 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 (Switzerland)
- 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 (Italy)
- 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 (Switzerland)
- 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 (Japan)
- OMWSA (detection of DNA repeats using moving window spectral analysis) Sydney (Australia)
- 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, see also 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 (Japan)
- 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 (Japan)
- 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 (Japan)
- 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 (Germany)
- 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 (French)
- 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 (Germany)
- 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 (French)
- 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 (Japan)
- PCMA (fast and accurate multiple sequence alignment based on profile consistency) Texas (USA)
- Pcons5 (combining consensus, structural evaluation and fold recognition scores) Stockholm (Sweden)
- 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 (French)
- PepSplice (cache-efficient search algorithms for comprehensive identification of tandem mass spectra) ETHZ (Switzerland)
- PERCH NMR Software Kuopio (Finland)
- 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 (French)
- PG (an efficient, versatile and scalable pattern growth approach to mine frequent patterns in unaligned protein sequences) Amsterdam (The Netherlands)
- PHIRE (a deterministic approach to reveal regulatory elements in bacteriophage genomes) Leuven (Belgium)
- 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 (Germany)
- Phylogenetic Analysis Computer Programs
- ALTree (association detection and localization of susceptibility sites using haplotype phylogenetic trees) Villejuif (French)
- APE (Analyses of Phylogenetics and Evolution in R language) Montpellier
- Auckland (Pebble including sUPGMA)
- California (HyPhy : maximum likelihood analyses)
- Connecticut
- Sanger (UK)
- Glasgow, see also
- Hennig
- 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
- Montreal (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 (Australia) (TreeCons, Hetero, BH, SeqVis, DMP, Symtest, BH+I, Homo)
- UCLA (BAli-Phy : simultaneous Bayesian inference of alignment and phylogeny) (USA)
- Vigo (Spain) (TreeScan, ProtTest, ModelTest, TCS, Geodis, SNPSim, Collapse)
- Washington, see also ATV
- Phylogenetic Tree Reconciler Lyon (French)
- PhyloGrapher (Graph Visualization Tool) Davis, see also ATGC (USA)
- Phylo_win (molecular phylogenetic inference) PBIL (France)
- PhylPro (detects genetic recombinations in homologous sequences) ANU (Australia)
- PipTools Software Package (alignments of similar regions in two DNA sequences) Pensylvania (USA)
- PIANA (protein interactions and network analysis) Barcelone (Spain)
- pIPHULA (parallel inference of population parameters using a likelihood approach) Vienna (Austria)
- PIVOT (protein interactions visualization tool) Tel Aviv (Israel)
- pknotsRG (RNA pseudoknot folding including near-optimal structures and sliding windows) Bielefeld (Germany)
- Plasmid Processor (W 95) Kuopio (Finland)
- PMcomp/PMmulti (alignment of structural RNAs) Vienna (Austria)
- 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 (Malaysia)
- PowQ (a user-friendly package for the design of variance component multipoint linkage analysis studies) London (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 (China)
- PREPI (molecular graphics program) BMM (UK), see also 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 (Germany)
- ProMoT/Diva (modular modeling of cellular systems) Magdeburg (Germany)
- 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) Warsaw (Poland)
- ProViz (protein interaction visualization and exploration) Bordeaux (French)
- 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 (Japan)
- PTG (a parsimonious tree-grow method for haplotype inference) Beijing (China)
- PubCrawler - an Update Alerting Service for PubMed and GenBank : perl script PubCrawler
- Publicly Available Software (ESTPrep, RHScorer, Clustering, UITagCreator) CLCG (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 (South Africa)
- 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 (Japan)
- pyzerg (python wrapper for the Zerg BLAST parser) Dundee (Scotland)
- QAlign (quality-based multiple alignments with dynamic phylogenetic analysis) Bielefeld (Germany)
- 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 (China)
- QTree (a program for generating CPK) UCL (UK)
- QuDA (the Qualitative Data Analysis Tool) Dresden (Germany)
- R/qtl (a QTL mapping environment) Johns Hopkins (USA)
- R'MES (Programs to Find Words with Unexpected Frequencies in DNA Sequences) INRA (French)
- 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 (Australia)
- Rapid (fast DNA database searching) Manchester (UK)
- RASCAL (rapid scanning and correction of multiple sequence alignments) Strasbourg (French)
- RasMol Berkeley, see also UMass, see also 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 (Switzerland)
- Recco (recombination analysis using cost optimization) Max-Planck (Germany)
- ReDiT (Repeat Discrepancy Tagger - A Shotgun Assembly Finishing Aid) Stockholm (Sweden)
- RCGScanner (analysis of regulon structures in different bacterial genomes) Barcelona (Spain)
- RDP2 (recombination detection and analysis from sequence alignments) Vigo (Spain)
- 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 (Korea)
- Repseek (a tool to retrieve approximate repeats from large DNA sequences) Jussieu (French)
- Rfold (an exact algorithm for computing local base pairing probabilities) Tokyo (Japan)
- 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 (French)
- Ribostral (an RNA 3D alignment analyzer and viewer based on basepair isostericities) BGSU (USA)
- RNA db tools BiRC (Denmark)
- RNALI (analyzes rRNA sequence) PBIL (French)
- 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 (Germany)
- RNAML (syntax for exchanging RNA information) Montreal (Canada)
- RNAMOT, ISOPAIR ESIL (French)
- RNAshapes (an integrated RNA analysis package based on abstract shapes) Bielefeld (Germany)
- R Package (Multidimensional analysis, spatial analysis) Montreal (Canada)
- RPMs (the newly released NCBI Blast and clustalw-1.81 code) Scalable Informatics
- rRNA Software (Ranfold, TreeCon) Antwerp (Belgium), see also RnaViz
- R/qtlbim (QTL with Bayesian Interval Mapping in experimental crosses) Madison (USA)
- RRTree (relative-Rate Tests with a tree) PBIL (French)
- S2S (display, manipulate and interconnect RNA data from sequence to structure) Strasbourg (French)
- SALTO (a structure-based method for protein sequence alignment) NCBI (USA)
- SARMENT (python modules for HMM analysis and partitioning of sequences) PBIL (French)
- 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 (Spain)
- Saturated BLAST La Jolla (USA)
- SBML ODE Solver Library (a native API for symbolic and fast numerical analysis of reaction networks) Vienna (Austria
- 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 (French)
- SEALS (A System for Easy Analysis of Lots of Sequences) NCBI (USA)
- SEAN (SNP prediction and display program utilizing EST sequence clusters) London (UK)
- SELFID (Self-identification of coding regions in microbial genomes) IGS (French)
- SEPON (a selection and evaluation pipeline for oligonucleotides) Tjele (Denmark)
- seq++ (analyzing biological sequences with a range of Markov-related models) Evry (French)
- 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) Lisboa (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 (Germany)
- SITEBLAST (rapid and sensitive local alignment of genomic sequences employing motif anchors) Max Planck (Germany)
- SlidingBayes (exploring recombination using a sliding window approach based on Bayesian phylogenetic inference) Leuven (Belgium)
- 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 (French)
- 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 (China)
- SOAP (cleaning multiple alignments from unstable blocks) IMBM (Belgium)
- 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 (French)
- 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, APV, 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 (Italy)
- 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 (Norway)
- SOLAR (Sequential Oligogenic Linkage Analysis Routines) SFBR
- SOMBRERO (finds regulatory elements in a set of DNA sequences) Galway (Ireland)
- 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 (Brasil)
- Sputnik (searches dna sequence for microsatellite repeats) Abajian (USA)
- SQUINT (a multiple alignment program and editor) Auckland (New-Zealand)
- SSAHA (tool for very fast matching and alignment of DNA sequences) Sanger (UK)
- S-SPatt (simple statistics for patterns on Markov chains) Evry (French)
- S-system (parameter estimation using Simulated Annealing for S-system models of biochemical networks) Munich (Germany)
- 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)
- Statistics of biological sequences (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 (Poland)
- Stormo Laboratory software (Consensus, Landscape, GenParser, PromFD, Co-Bind, PhyloCon) St Louis (USA)
- STRAL (progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time) Dusseldorf (Germany)
- 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 (China)
- 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 (French)
- TESD (a transposable element dynamics simulation environment) PBIL (French)
- T-REX (Tree and reticulogram Reconstruction) Montreal (Canada)
- Terminus (telomeric end-read mining in unassembled sequences) Kentucky (USA)
- TFBS (Perl modules for transcription factor detection and analysis) Stockholm (Sweden)
- THESEUS (maximum likelihood superpositioning and analysis of macromolecular structures) Colorado (USA)
- THESIAS (testing haplotype effects in association studies) Paris VI (French)
- 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) Pavia (Italia)
- TINKER St. Louis (Molecular Modeling Package), distribution of PROPAK, SLEUTH, QSAR, GETPDB
- TIP (protein backtranslation aided by genetic algorithms) Santiago (Chile)
- Titri (Enzyme Linked Immuno Assay calculations) Vidarsson
- ToolDiag (pattern recognition toolbox) UFES (Brasil)
- TOPD/FMTS (a new software to compare phylogenetic trees) Tarragona (Spain)
- TOPP (the OpenMS proteomics pipeline) Tubingen (Germany)
- TOPAL (detecting mosaic sequences and rate heterogeneity in phylogenetic datasets) BioSS (UK)
- TopoICE-R (3D visualization modeling the topology of DNA recombination) Iowa (USA), another link
- TRA (software program combining sequence motif searches with keywords for finding repeats containing DNA sequences) Antalya (Turkey)
- TraceEdit (a DNA trace editor and viewer) Wurzburg (Germany)
- Transterm (rho-independent transcription terminators in bacterial genomes) Maryland (USA)
- TRAP (predicting transcription factor affinities to DNA from a biophysical model) Berlin (Germany)
- TREBLE (tree and rate estimation by local evaluation of heterochronous nucleotide data) California (USA)
- Treefinder (phylogenetic trees from nucleotide sequences) Gangolf (Germany)
- 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 (Germany)
- TreeQ-VISTA (an interactive tree visualization tool with functional annotation query capabilities) California (USA)
- TreeSnatcher (coding trees from images) Vienna (Austria)
- TreeView X Glasgow (UK)
- TRFMA (a web-based tool for terminal restriction fragment length polymorphism analysis based on molecular weight) Fukuoka (Japan)
- TribeMCL (method for clustering proteins into related groups) EBI (UK)
- TRNinfer (inferring transcriptional regulatory networks from high-throughput data) Osaka (Japan)
- 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 (Australia)
- 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) Varsaw (Poland)
- Unrooted (tree drawing program) PBIL (French)
- USC Computational Biology Software Packages (Alignment, Chimera, DNA spectrum, Procrustes,..) USC (USA)
- USF software (Macromolecular Crystallography and Structural Biology) Uppsala (Sweden)
- VariScan (analysis of evolutionary patterns from large-scale DNA sequence polymorphism data) Barcelona (Spain)
- VEIL (hidden Markov model for finding genes in vertebrate DNA) TIGR (USA)
- VEMS (interpreting peptide mass spectra) Aalborg (Denmark)
- 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 (Austria)
- 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 (French)
- VizRank (finding informative data projections in functional genomics by machine learning) Ljubljana (Slovenia)
- VMD (visual molecular dynamics) Illinois (USA)
- Voro3D (3D Voronoi tessellations applied to protein structures) Jussieu (French)
- W2H (WWW Interface to the GCG Sequence Analysis Software Tools) EBI
- Watson (statistical test to detect genetic divergence among populations from DNA fingerprinting data) Pavia (Italy)
- 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 (New Zealand)
- wEMBOSS (a web interface for EMBOSS) La Plata (Argentina)
- 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 (Switzerland)
- Wrapping up BLAST and other applications for use on Unix clusters Dublin (Ireland)
- XAct (maintain and record the results of crystallisation experiments) Aarhus (Denmark)
- 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 (French)
- YASS (local alignment of DNA sequences) LIFL (French)
- Zerg (a very fast BLAST parser library written in C) Sao Paulo (Brasil)
- ZFIQ (a software package for zebrafish biology) China
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