Databases and Analysis tools by ftp
Original Site: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
- Weizmann :
bioinformatics.weizmann.ac.il
- Specialized sites or out of archive
- ABBESS (Approximation of the Basic Bayesian Evidence for Sequence Segmentation) BioSS (UK)
- ACEDB, AcePerl ... CSHL, see also acedb
- 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)
- AL2CO (Calculates Positional Conservation in a Protein Sequence Alignment) Texas (USA)
- ALGGEN (Algorithmics and Genetics : Dotlet) Barcelona (Spain)
- AlignACE Harvard (USA)
- Alignment Editors SeaView (France)
- AlphaSimp (Simplifying amino acid alphabets by means of a branch and bound algorithm and substitution matrices) CRIBI (Italy)
- AMBER (Assisted Model Building with Energy Refinement) UCSF
- AMSOL (SCF Program for Free Energies of Solvation) UMN (USA)
- Andrew Martin's page (Torsions, ProFit, QTree, MINT, Cluster)
- Angler: A Browser of C.elegans Embryo Development In Time and Space Sanger (UK)
- ANTHEPROT (DOS, WINDOWS et IBM rs6000) PBIL (France)
- Apollo (Drosophila Genome Browser) Ensembl, see also BDGP
- ARB (A Software Environment for Sequence Data) Max-Planck, see also (Germany)
- 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)
- AutoDock (automatic docking of flexible ligands to macromolecules) SRI (USA)
- BALL (Biochemical Algorithms Library) Max-Planck (Germany)
- 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)
- BioArray (a tool to analyze macroarray images) Hertfordshire (UK)
- BIODEV (MatInd, ConsInspector, CoreSearch, GenomeInspector, FastM, Model generator, DIALIGN) BIODEV (Germany)
- BioEdit (user-friendly sequence alignment editor which runs on W95, W98, NT) North Carolina (USA)
- Bioinformatics Lab (Euler, Grimm, MGR, MultiProfiler) UCSD (USA)
- Bioinformatics Research Group (Arcade, Genoma map viewer, Gridmap, Plasmid drawing) JIC (UK)
- Bioinformatics software Bioinformatics
- Bioinformatics source SourceForge
- BioJava (open-source project) BioJava.org
- BioLayout (An automatic graph layout algorithm for similarity visualization) EBI (UK)
- Biological Data Representation and Query (QuickPDB, MMQL, MEME, etc..) SDSC (USA)
- Biological software developed at Pasteur Institute (French)
- Biology Debian package Pasteur (France)
- Biomer (Java-based on-line biomolecular modeling package) SRI (USA)
- Bioperl Proposal for Perl5 Objects for Sequences, Alignments, and Phylogenies Georg Fuellen (VSNS : Germany), see also BioPerl
- BioTEX (LaTex2 bio extensions) Tuebingen (Germany)
- BioWidgets Consortium (Graphical displays of genome data) Berkeley (USA)
- BioWidgets for Java CBIL (USA)
- BLAST et BLAST2.0.2 NCBI (USA)
- BLAST2 Wu-archives (USA)
- WebBLAST2 NHGRI (USA)
- BRAGI (protein modelling and display program) GBF (Germany)
- BTL (Bioinformatics Template Library) Birbeck (UK)
- Calign (aligning sequences with restricted affine gap penalties) Indiana (USA)
- CAP (Contig Assembly Program) CSD (USA)
- CARD (program for drawing RNA secondary structure models) Antwerp (Belgium)
- CASA (Critical Assessment of Sequence Alignment Accuracy) DBI (USA)
- Case group (Amber, Nabs, Rnamotif, Shifts) SRI (USA)
- CBIL Tools (GenLang, BioWidgets, TESS, CPL) CBIL (USA)
- CBS Software CBS : Signal Scan - Promoter Scan (Minnoseta)
- CCMS Software (Xtalview, Shape...) SDSC (USA)
- 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)
- ChemWeb (to draw chemical structures) SoftShell (USA)
- Chime Resources Massachusetts (USA)
- Circles (comparative analysis of RNA secondary structure) Glasgow (UK)
- CITA (programming interface that allows access to one or more ACEDB databases through CORBA) JIC (UK)
- CloneIt: finding cloning strategies, in-frame deletions and frameshifts INRA (France)
- ClustalX (ClustalW with graphical interface : Unix, NT, Macintosh) Strasbourg (France)
- Cn3D (a 3D molecular structure viewer and W3 helper (Entrez)) NCBI
- 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)
- Computational Biology Group - DAIMI (ComAlign, CombAt, HMMComp, Hudson, RecPars, StatAl) Aarhus (Denmark)
- 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)
- CoPE (a Collaborative Pedigree Environment) InfoBioGen (France)
- CORBA-Java based Application Wrapper EBI (UK)
- CpGProD (CpG Island Promoter Detection) PBIL (French)
- CS-PSeq-Gen (Simulation of protein sequences under constraints) Jussieu (French)
- DaliLite (pairwise structure comparison and database searching) EBI
- DAMBE (Data Analysis in Molecular Biology and Evolution) Hong Kong
- Darwin CBRG (Switzerland)
- DBsolve (software for metabolic, enzymatic and receptor-ligand binding simulation) GRMC (USA)
- Detection and analysis of synaptic events in intracellular electrophysiological recordings Pasteur (French)
- DIALIGN (alignment of nucleic acid and protein sequences) BIODV (Germany)
- DICOPROT (DICHROism of PROTeins) IBCP (French)
- DINO (Visualizing Structural Biology) Biozentrum (Switzerland)
- DIVCLUS (protein sequence domain clustering program) MRC (UK)
- DNAPlot (Mac, PC, Unix) Cologne (Germany), see also
- DnaSP, DNA Sequence Polymorphism Barcelona (Spain)
- DOCK (Molecular docking simulations) UCSF (USA)
- Domain Finder (characterization of dynamical domains in proteins) Orléans (French)
- Double Digester www (Yale)
- Duke Bioinformatics Shared Resource (TreeMap, ClusterView, AnnotatorProgram, GenePlacer, ConduitBrowser, HomoloGeneBrowser, SeqWebHub, BlastWeb) Duke (USA)
- DUST filter (Tatusov, Lipman) WUSTL
- Dynafit P. Kuzmic (USA)
- Dynamite (code generating language developed for sequence comparison) Sanger (UK)
- 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)
- EDIBLE (Experimental Design and Information By Likelihood Exploration) Cambridge (UK)
- EMBOSS EMBNet UK
- Emerge (middleware components : search services is through platform-neutral standard and emerging-standard tools such as Z39.50, XML, and Java) NCSA (USA)
- Eponine (mammalian transcription start sites) Sanger (UK)
- ERPIN (Easy RNA Profile IdentificatioN) TAGC (French)
- ESSA (RNA secondary structure analysis) INRA (France)
- ESTate (Expressed Sequence Tag Analysis Tools) HGMP (UK)
- Evolutionary HMMs (a Bayesian approach to multiple alignment) LANL (USA)
- ezDB (sequence database software) Oxford (UK)
- FADE and PADRE (Atomic Density Methods for Molecular Shape and Shape Complementarity) SDSC (USA)
- FALCON (Fast Assemblies of Large Contigs) www (Harvard)
- 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) ISM (Japan)
- FlexStab (calculates helix stability and flexibility of a given DNA sequence) Kerem (Israel)
- Flow Cytometry www (Salk)
- Folding@home (simulates protein folding ("distributed dynamics")) Stanford (USA)
- Free Flow Cytometry Software Purdue (USA)
- freqA (identification of putative programmed translational frameshift sites) Utah (USA)
- FROST (fold recognition program) INRA (French)
- 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)
- GEANFAMMER (GEnome ANalysis and Protein FAMily MakER) MRC (UK)
- GePCR (Graphical front-end for electronic PCR) Nice (French)
- Gene-finding and machine learning systems (VEIL, MORGAN, OC1, PEBLS, Glimmer) TIGR (USA)
- GeneMachine (integrated tool intended to perform both comparative and predictive gene identification) NHGRI (USA)
- GeneMine (sequence analysis and visualization program) UCLA (USA)
- GeneRAGE (algorithm for sequence clustering and domain detection) EBI (UK)
- Genetic Analysis Software (FastLink, MSA, CASPAR, PedHunter, CGH, Mapping) NCBI (USA)
- GeneX (Internet available repository of gene expression data) NCGR
- Genexp (tool for simulation of dynamics of genetic regulatory networks) Prague (Czech Republic)
- GenLang (tRNA, group I intron, protein gene : "Linguistic Methods") CBIL (Pennsylvania)
- Genotype Transposer IARC (French)
- Gepasi (Biochemical simulation) Aberystwyth (Wales)
- GFF: an exchange format for gene-finding Sanger (UK)
- Ghemical (computational chemistry software package released under the GNU GPL) Kuopio (Finland)
- GNA (tool for the modeling and simulation of genetic regulatory systems) INRIA (French)
- GOLD (Graphical Overview of Linkage Disequilibrium) Oxford (UK)
- GPRIME (PCR primers tools) ANU (Australia)
- Grappe (fast searching a text file for regular expressions) Loria (French)
- GRASP (Graphical Representation and Analysis of Structural Properties) Columbia (USA)
- GUS (Genomics Unified Schema) CBIL (USA)
- HMM (PASSML and PASSML-TM) Cambridge (UK)
- HMMCOMP (Comparison of hidden Markov models) Aarhus (Denmark)
- HMMER Washington (USA)
- HONIG Lab software (DelPhi, MCCE, Energy functions, SCAP, Loopy, Spin-PP, GRASP, GRASS,..) Columbia (USA)
- Html4blast Pasteur
- Imagene Notebook (cooperative computer environment for the annotation and analysis of genomic sequences) Jussieu (French)
- IMP services (GPI predictor, SSCP, NSC,..) IMP (Austria)
- Ingenenue (Genetic Network Construction Software) NSF (USA)
- InterProScan Package EBI (UK), see also
- 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)
- Java-based Molecular Biology Work Bench EMBL (Alignment Editor, Pattern Searching, PCR, pI, Oligo, Map, Translate, ..)
- Jeff's Perl Programs CWRU (USA)
- JESAM (CORBA software components to create and publish EST alignments and clusters) EBI (UK)
- Jnet (Neural Network Protein Secondary Structure Prediction Method) EBI (UK)
- JTEF (3' terminal exon finder for human DNA sequences) CSHL (USA)
- 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)
- LVB (reconstructing evolution with parsimony and simulated annealing) Reading (UK), see also RDG
- MACAW (program for locating, analyzing, and editing blocks of localized sequence similarity) NCBI (USA)
- MacroModel www (An Integrated Software System for Modeling Organic and Bioorganic Molecules Using Molecular Mechanics)
- MacStripe (Prediction of Coiled Coils) York (UK)
- MAGPIE (Automated Genome Project Investigation Environment) Rockfeller (USA)
- 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
- Maptools (programs for working with experimental three-dimensional (density) maps) Gottingen (Germany)
- Martin group software (PC : ProfCheck, START, Sequence comparator, Polymorph, Splits Tree Editor) Oxford (UK)
- MassXpert (predicting and analysing mass spectrometric data) Bordeaux (French), see also PolyXmass
- 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)
- MC-SYM (Nucleic acids 3D-structure prediction) MC-SYM (Canada)
- MCell (A General Monte Carlo Simulator of Cellular Microphysiology) Salk Institute (USA), another link
- 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) Berlin (Germany)
- Microarray
- AMADA (Analyzing Microarray Data) Hong Kong
- Base (manage the massive amounts of data generated by microarray analysis) Lund (Sweden)
- Bioconductor Harvard
- FuzzyART (Analysis of expression profile using fuzzy adaptive resonance theory) Nagoya (Japan)
- GeneViz Munich (Germany)
- 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)
- MGED Software (Microarray Gene Expression) MGED
- Marray (analysing single, replicated or reversed microarray experiments) Oslo (Norway)
- Maxd Manchester
- Oliz (Perl scripts that selects 50mer oligonucleotides for use in DNA microarrays) UTMEM (USA)
- P-Scan (Microarray : Peak quantification using Statistical Comparative ANalysis) NIH (USA)
- Plant-Arrays Software Montpellier (French)
- R package (Statistics for Microarray Analysis) Berkeley
- YASMA Birbeck
- R Packages For Gene Expression Analysis (links) Munchen
- Microarray analysis and database softwares comparison YLF
- Microbiological software (MSDOS) www (Southampton), another link
- MIG software (Frost, Island, MuGeN, R'Hom, R'Mes) INRA (French)
- Miropeats (sequence similarity amongst any set of DNA sequences) EBI (UK)
- MMTK (Molecular Modelling Toolkit) Orléans (French)
- MMTSB software (Modelling package, Tool set, Yammp) SRI (USA)
- Modelisation (genetic et molecular) : (R'MES, R'PRO, SliceEMBL, SeqFold) BIA (French)
- Modeller (program for homology protein structure modelling by satisfaction of spatial restraints) Rockefeller (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 (Netherlands)
- MOLDY (molecular dynamics simulation) Oxford (UK)
- Molecular Biological Software (annotate, createGel, Webblast...) Toronto (Canada)
- Molecular Biology related programs for Linux BioInf
- Molecular Neurobiology (Melting, Cosindex, Compacc, Clu2nssp) Pasteur (French)
- Molekel (molecular visualization package) CSCH (Switzerland)
- MolMol (MOLecule analysis and MOLecule display) ETHZ (Switzerland)
- MOLPHY (Computer Program Package for Molecular Phylogenetics) Tokyo (Japan)
- Molscript Avatar
- MPEx (Membrane Protein Explorer) Irvine (USA)
- MPSA (Multiple Protein Sequence Analysis) PBIL (French)
- MrBayes (Bayesian inference of phylogeny) Uppsala (Sweden)
- MSTAT (nonparametric statistical methods) Wisconsin (USA)
- Multivariate analysis and graphical display software package for Macintosh and PC (NetMul, MacMul, GraphMu, MacDendro, ADE-4) Lyon (France)
- Multivariate analysis software Oklahoma (USA)
- Mview (tool for converting the results of a sequence database search into the form of a coloured multiple alignment) EBI (UK)
- Naccess (Atomic Solvent Accessible Area Calculations) UMIST (UK)
- NAMOT (Nucleic Acid MOdeling Tool) www (Los Alamos)
- NJplot (tree drawing program) PBIL (France)
- NetBuilder (graphical tool for representing and simulating genetic regulatory networks) Hertfordshire (UK)
- Neural Networks at your Fingertips Geocities (USA)
- NEURON (simulator of neurons and networks) North Carolina (USA)
- Novella (a bridge project) EBI (UK)
- Oligo (binding reactions needed to make protein oligomers) Cambridge (UK)
- OpenBSA (freely available implementation of the Biomolecular Sequence Analysis) EBI (UK)
- 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)
- ORI-GENE (tool for Gene Classification Based on the Evolutionary Tree) Riken (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)
- Packages for life science MathSource (USA)
- PAL (Java library for researchers in molecular phylogenetics) Pal-project
- Palingol Jussieu (French)
- PAML (Phylogenetic Analysis by Maximum Likelihood) UCL (UK)
- PARS (Positional Analysis of Regulatory Sequences) Hertfordshire (UK)
- PDAP (PHENOTYPIC DIVERSITY ANALYSIS PROGRAMS) Wisconsin (USA)
- PERCH NMR Software Kuopio (Finland)
- Perl as a Tool for Linkage Analysis Rockfeller (USA)
- Perl Modules Sanger (UK)
- Phrap and Phred (Fast sequence assembly) Phrap (USA)
- Phylogenetic Analysis Computer Programs
- Auckland (Pebble including sUPGMA)
- Connecticut
- Sanger (UK)
- Glasgow, see also
- Hennig
- Huelsenbeck software (CodonBootstrap, MrBayes, Siminator) Rochester (USA)
- Ilinois (fastDNAml)
- LANL (Weighbor: weighted version of Neighbor Joining)
- LMS (PAUP)
- Lyon (NetMul, MacMul, GraphMu, MacDendro, ADE-4)
- Manchester (PHASE : Phylogenetics and Sequence Evolution)
- MEP
- Montpellier (QR2, BioNJ, Q*, Gamma, DTscore, FastME, Model Trees)
- Oxford (UK) (Unix, Macintosh)
- Pasteur (Taxotron software for Macintosh)
- PennState
- Pusan (Phylodraw)
- Washington, see also ATV
- 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)
- Plasmid Processor (W 95) Kuopio (Finland)
- PolyXmass (mass spectrometric data analysis) Polyxmass
- PovChem (molecular graphics) Johns Hopkins (USA)
- Ppovit (reads 3-D molecular structure coordinates in PDB) Michigan (USA)
- PREPI (molecular graphics program) BMM (UK)
- Primer MIT (USA)
- PROCHECK (checks the stereochemical quality of a protein structure) UCL (UK)
- Promoter Extraction from GenBank (PEG) CSHL
- PROMSCAN (predicts sigma54-dependent promoters) uklinux
- PROSEQ (equence editing and population genetics, (mol/evol) analysis) Edinburgh (UK)
- PROSPECT (PROtein Structure Prediction and Evaluation Computer Toolkit) ORNL (USA)
- PSIPRED (Secondary structure prediction) UCL (UK)
- PubCrawler - an Update Alerting Service for PubMed and GenBank : perl script PubCrawler
- Publicly Available Software (ESTPrep, RHScorer, Clustering, UITagCreator) CLCG (USA)
- Python base software MGL (USA)
- Python-based software for life science research BioPython (USA)
- QFC (Quasi-Periodic Feature Classifier algorithm for G protein-coupled receptors) Yale (USA)
- QTDT (Linkage Disequilibrium Analyses for Quantitative Traits) Oxford (UK)
- QTL Cartographer (a suite of programs to map quantitative traits using a map of molecular markers) North Carolina (USA)
- QTree (a program for generating CPK) RUBiC
- R'MES (Programs to Find Words with Unexpected Frequencies in DNA Sequences) INRA (French)
- RAPDistance Package ANU (Australia)
- Rapid (fast DNA database searching) Manchester (UK)
- RasMol Roger Sayle, mirror at Berkeley, see also UMass, see also Open RasMol
- RHOM (Research of HOMogeneous regions in DNA sequences) INRA (French)
- 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)
- RNAMOT, ISOPAIR ESIL (French)
- R Package (Multidimensional analysis, spatial analysis) Montreal (Canada)
- RPMS (Grace and TreeTool) for the Linux RedHat platform Snafu (Germany)
- rRNA Software (DCSE, RnaViz, TreeCon) Antwerp (Belgium)
- RRTree (relative-Rate Tests with a tree) PBIL (French)
- SAM (Sequence Alignment and Modeling System) www
- SAT (sequence search algorithm assessment and testing toolkit) MRC-LMB (UK)
- Saturated BLAST La Jolla (USA)
- SCI Software (SCIrun, Map3d, BioPSE, Unintah, VISPack) UTAH (USA)
- SeaView (graphical multiple sequence alignment editor) PBIL (French)
- SEALS (A System for Easy Analysis of Lots of Sequences) NCBI (USA)
- SELFID (Self-identification of coding regions in microbial genomes) IGS (French)
- SEQIO
ftp.cs.ucdavis.edu under pub/strings/, documentation Pasteur
- Sequencing Software Sanger (UK)
- Shady Box (multiple sequence alignment drawing program (Unix)) ANGIS (Australia)
- SIM4 (to align cDNA and genomic DNA) Pennsylvania (USA)
- SISEQ (simple sequence manipulation tool) MPL (Japan)
- SMILE (tool that infers motifs in a set of sequences) IGM (French)
- SOAP (cleaning multiple alignments from unstable blocks) IMBM (Belgium)
- SOAP-based Analysis Web Service EBI (EBI)
- Software at Caltech (USA)
- Software (QTree, ProFit, MINT, NW, Torsions) at RUBiC
- Software at Sanger Centre Sanger (UK)
- Software (Chasalow, ComBin, Crooschecker, CGT, Kweker, MQA, MapComp, PhylTools, Splitloc, BCSIM) Wageningen (Netherlands)
- Software at WashU (Hmmer, Pfam, Atv, Cove, TrnaScan, RnaBob, Suqid, Qrna, PkNots) Washington (USA)
- Software for Biology (PC) ANNHYB (France)
- Software for structure determination and analysis PDB (USA)
- Software from the Department of Human Genetics (APM, FastSLINK, MEGA2, Pedcheck, Simibd,..) Pittsburgh (USA)
- Smarties (A.B.I. Curie) :
ftp.curie.fr under pub/jompo/sma/
- SPLASH (Structural pattern localization analysis by sequential histogram) IBM (USA)
- Sputnik (searches dna sequence for microsatellite repeats) Abajian (USA)
- SSAHA (tool for very fast matching and alignment of DNA sequences) Sanger (UK)
- SSMAL (Shuffled Similarities with Multiple ALignments) TBI (Germany)
- Staden Package WWW site
- 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), see also Pasteur
- STOCKS (STOChastic Kinetic Simulation of biochemical processes with Gillespie algorithm) Warszawa (Poland)
- Stormo Laboratory software (Consensus, Landscape, GenParser, PromFD, Co-Bind) St Louis (USA)
- 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
- Taxonomic Markup Language (XML) Albany (USA)
- T-COFFEE (Multiple Alignments) IGS (French)
- T-REX (Tree and reticulogram Reconstruction) Montreal (Canada)
- TFBS (Perl modules for transcription factor detection and analysis) Stockholm (Sweden)
- THREADER (predicting protein tertiary structure by recognizing the correct fold from a library of alternatives) Version 2.5 (UK)
- TIGR Software Tool Collection (ADE, btab, MSA, Assembler, Glimmer, yank ...) TIGR (USA)
- TINKER St. Louis (Molecular Modeling Package), distribution of PROPAK, SLEUTH, QSAR, GETPDB
- Titri (Enzyme Linked Immuno Assay calculations) Vidarsson
- ToolDiag (pattern recognition toolbox) UFES (Brasil)
- TOPAL (detecting mosaic sequences and rate heterogeneity in phylogenetic datasets) BioSS (UK)
- Transterm (rho-independent transcription terminators in bacterial genomes) TIGR (USA)
- Tree-Puzzle (Maximum likelihood analysis for nucleotide, amino acid, and two-state data) Leipzig (Germany)
- TreeView X Glasgow (UK)
- TrExML (phylogenetic program for maximum likelihood analysis of nucleotide sequences) Angis (Australia)
- UCSF Public Resources (Protein Modeling) Fred Cohen Laboratory (USA)
- 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)
- VEGA (a program to convert, manage, vizualise 3D structures) Milano (Italy)
- VEIL (hidden Markov model for finding genes in vertebrate DNA) Johns Hopkins (USA)
- Vienna RNA Package Vienna (Austria)
- VisBio (biological visualization tool designed to allow easy visualization and analysis of 4-D multispectral data) Wisconsin (USA)
- VISTA (VISualization Tool for Alignments) LBL (USA)
- 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)
- 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)
- WinPep (a versatile tool for the analysis of aminoacid sequences) ETHZ (Switzerland)
- WWW search Pub-Med : perl module CPAN
- 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 (France)
2002