AbOrygen : Intuitive bioinformatics AbOrygen develops the next generation of bioinformatics software with powerful new features that simplify and improve the research work of life scientists worldwide.
AcaClone pDRAW32 Freeware DNA cloning, analysis and visualization software.
AnnHyb - Nucleotidic Sequence Manager Free software for working with and managing nucleotide sequences in multiple formats. Many features including sequence annotation, restriction analysis, pattern searching, retrieval from servers. Released under GNU Public Licence.
ARCiB -- Accessible Retired Computers in Biology NSF supported project to make old computers accessible to new software in bioinformatics. Provides transitional and supplemental support, especially in structual biology, for software packages on various platforms.
Array Genetics Bioinformatics programs, including MendelBase.
Array Genetics, Inc. Provider of software solutions to meet the needs of researchers seeking to extract information from genome sequencing projects and DNA microarray screening. Free access to SeqIt, an on-line protein database mining program.
Artemis Software Available from the Sanger Institute of the Wellcome Foundation, is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses.
Computer Program for Polyphasic Taxonomy Analysis The proBiosys suite of programs compares phenetic, chemotaxonomic and nucleic acid sequence data. Algorithms for polyphasic taxonomy are available to construct Dendrograms, the suite is simple to use.
DARWIN An interactive tool for peptide and nucleotide sequence analysis
DNA-Star - Lasergene Commercial sequence analysis and manipulation suite for Windows and Macintosh.
DNAStar Develops sequence analysis software for molecular biology.
EMBOSS The European Molecular Biology Open Software Suite. An open source project started by the EMBnet community in order to replace proprieatry systems like GCG.
GDE for Linux An integrated linux environment for bioinformatics and evolutionary analysis based on the Genetic Data Environment (GDE). Contains binaries for Linux and Mac OS X, documentation, screenshots, references, and organism specific interfaces.
Gene Expression Data Analysis web application Normalization tests for differentially expressed genes, clustering, bootstrapping, leave-one-out validation, cross-fold validation, and links to external genomic databases.
GeneRunner for Windows A fairly old sequence analysis tool for everyday lab use. Formerly a commercial product - now "abandonware."
GeneticXchange Data access and integration software for the life sciences industry.
GeneticXchange Software for life science discovery; enterprise-level data integration and desktop biologists.
Gints Object-oriented regulation network simulator written in Java. Includes downloadable software and documentation. The site is in French and English.
HMMER Sean Eddy's lab, present profile hidden Markov models for biological sequence analysis, a tool used to build HMMs from multiple alignments, and calculate e-scores.
Logical Depth Accelerated sequence analysis tools for HMMsearch and Smith-Waterman.
Lucid A system for creating, maintaining, distributing and playing interactive identification keys.
LucID Professional Software for creating interactive keys for biology, taxonomy, medicine, and agriculture.
Meta-MEME v2.0.1 Software toolkit for building and using motif-based hidden Markov models of DNA and proteins - from the Univ. of California-San Diego.
Meta-MEME v2.0.1 Software toolkit for building and using motif-based hidden Markov models of DNA and proteins - from the Univ. of California-San Diego.
Meta-MEME v2.0.1 Software toolkit for building and using motif-based hidden Markov models of DNA and proteins - from the Univ. of California-San Diego.
Metalifesocieties Makes available various bioinformatics algorithms, which perform all essential tasks in sequence analysis and sequence-based predictions.
NCBI BLAST BLAST (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases regardless of whether the query is protein or DNA.
Premier Biosoft International Developers of software for real time PCR primer design, TaqMan, molecular beacons, DNA microarray analysis, drawing restriction plasmid maps, gateway cloning experiments, protein interaction network and functional genomics.
Sequence Analysis for Mac OS X A freeware Mac OS X application written in Java that does many standard types of DNA and protein sequence analysis tasks.
Sight Extendable parallel system for automatic genome analysis. Software for analysing all potential genes in a defined genome region. Given two marker names, can output reports of genomic features between them. Features for converting between naming systems, sequence retrieval, E-PCR, gene prediction, similarity search, protein pattern search, and report formatting. Written in Java.
STRING Search for Tandem Repeats IN Genomes -- Includes C source code and examples.
The ARB Project A free sequence database application for Unix. It includes a sequence editor, several sequence aligners, phylogeny reconstruction tools, probe/primer search and generation, genome annotation and visualization. In addition to the integrated user-interface the ARB database can be accessed using Perl or C.
The Sanger Centre: Software Production software used at the Sanger Centre, physical mapping software, informatics and analysis software, and data formats
Verbumculus Genetic Sequence Analyzer An interesting tool to discover and visualize over- or under-represented words in genetic sequences. Executable for Sparc-Solaris, Sparc-Intel or Linux-Intel. Also available as a Java applet.
Verbumculus Genetic Sequence Analyzer An interesting tool to discover and visualize over- or under-represented words in genetic sequences. Requires Java support in browser. Also available as a downloadable program.
WU-BLAST Archives WU-BLAST: The Washington University BLAST. "...faster at any sensitivity, more sensitive at any speed, the first BLAST with gapped alignments and statistics."
XDigitize A visualization software system for evaluation of hybridisation experiments.
