- XDigitize - http://www.molgen.mpg.de/~xdigitise/
A visualization software system for evaluation of hybridisation experiments.
- Premier Biosoft International - http://www.PremierBiosoft.com
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.
- Meta-MEME v2.0.1 - http://metameme.sdsc.edu/
Software toolkit for building and using motif-based hidden Markov models of DNA and proteins - from the Univ. of California-San Diego.
- Computer Program for Polyphasic Taxonomy Analysis - http://www.proBiosys.com
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.
- The Sanger Centre: Software - http://www.sanger.ac.uk/Software/
Production software used at the Sanger Centre, physical mapping software, informatics and analysis software, and data formats
- NCBI BLAST - http://www.ncbi.nlm.nih.gov/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.
- WU-BLAST Archives - http://blast.wustl.edu/
WU-BLAST: The Washington University BLAST. "...faster at any sensitivity, more sensitive at any speed, the first BLAST with gapped alignments and statistics."
- GeneRunner for Windows - http://www.generunner.com
A fairly old sequence analysis tool for everyday lab use. Formerly a commercial product - now "abandonware."
- DNA-Star - Lasergene - http://www.dnastar.com/
Commercial sequence analysis and manipulation suite for Windows and Macintosh.
- DARWIN - http://cbrg.inf.ethz.ch/Darwin/index.html
An interactive tool for peptide and nucleotide sequence analysis
- GDE for Linux - http://www.bioafrica.net/GDElinux/index.html
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.
- GeneticXchange - http://www.geneticxchange.com/
Software for life science discovery; enterprise-level data integration and desktop biologists.
- AcaClone pDRAW32 - http://www.acaclone.com
Freeware DNA cloning, analysis and visualization software.
- Verbumculus Genetic Sequence Analyzer - http://www.cs.ucr.edu/~stelo/Verbumculus/
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.
- Metalifesocieties - http://metalifesocieties.tripod.com/
Makes available various bioinformatics algorithms, which perform all essential tasks in sequence analysis and sequence-based predictions.
- Sequence Analysis for Mac OS X - http://www.informagen.com/SA/
A freeware Mac OS X application written in Java that does many standard types of DNA and protein sequence analysis tasks.
- The ARB Project - http://www.arb-home.de
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.
- STRING - http://www.caspur.it/~castri/STRING/
Search for Tandem Repeats IN Genomes -- Includes C source code and examples.
- Gints - http://gints.free.Fr
Object-oriented regulation network simulator written in Java. Includes downloadable software and documentation. The site is in French and English.
- AnnHyb - Nucleotidic Sequence Manager - http://bioinformatics.org/annhyb/
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.
- LucID Professional - http://www.lucidcentral.com/
Software for creating interactive keys for biology, taxonomy, medicine, and agriculture.
- Sight - http://bioinformatics.org/jSight/
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.
- EMBOSS - http://www.rfcgr.mrc.ac.uk/Software/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.
- Array Genetics - http://www.arraygenetics.com/product_overview.php3
Bioinformatics programs, including MendelBase.
- AbOrygen : Intuitive bioinformatics - http://www.aborygen.com
AbOrygen develops the next generation of bioinformatics software with powerful new features that simplify and improve the research work of life scientists worldwide.
- ARCiB -- Accessible Retired Computers in Biology - http://arcib.dowling.edu/
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.
- limmaGUI - http://bioinf.wehi.edu.au/limmaGUI/index.html
A graphical user interface for linear modelling of cDNA and oligonucleotide microarray data to identify differentially expressed genes.
- Gene Expression Data Analysis web application - http://bioinformatics.upmc.edu/GE2/GEDA.html
Normalization tests for differentially expressed genes, clustering, bootstrapping, leave-one-out validation, cross-fold validation, and links to external genomic databases.
- JAligner - http://jaligner.sourceforge.net/
Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment.
- Logical Depth - http://logicaldepth.com/
Accelerated sequence analysis tools for HMMsearch and Smith-Waterman.
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