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• AcaClone pDRAW32 - Freeware DNA cloning, analysis and visualization software.
• AG BIODV Software - Links to software developed by the AG BIODV group. Tools for consensus, alignment and definition. Both downloads and executables.
• 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.
• Array Genetics - Bioinformatics programs, including MendelBase.
• Artemis: A DNA Sequence Viewer and Annotation Tool - Java program to display a DNA sequence, annotated with features, ORFs. Reads many input formats.
• BSML - Bioinformation Sequence Markup Language - Extensible language specification and container for bioinformatic data.
• 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.
• 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.
• Genalysis Genome Analysis Toolkit - Commercial tool for comparing whole genomes or large genetic sequences. Outputs lists of matches and dot-plots and supports web-based BLAST searches.
• GeneRunner for Windows - A fairly old sequence analysis tool for everyday lab use. Formerly a commercial product - now "abandonware."
• 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 - profile hidden Markov models for sequence analysis - Sean Eddy's tools to build HMMs from multiple alignments, align sequences to HMMs, calculate e-scores, and other tools
• Linux Software Encyclopedia - Bioinformatics - Links to Bioinformatics software for Linux. From the Linux Software Encyclopedia.
• 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.
• Molecular Evolutionary Genetics Analysis (MEGA2) software - Provides free downloadable MEGA2 software for use in comparative sequence analysis of genetic data. Program for Win32 platforms.
• 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.
• Paracel BLAST - Software for accelerated parallel BLAST searching
• PHRED - Base-Calling Software with Quality Information - A widely-used program for calling DNA sequence bases from sequencer trace files.
• Phred/Phrap/Consed System Home Page - basecaller / assembler / sequencer finisher and related tools from the UW Genome Center.
• 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.
• PubCrawler - An Update Alerting Service for PubMed and GenBank - Software and an online service for periodically performing predefined searches at NCBI, reporting new results by email or on the web.
• Public Domain Software in Biology - The aim of this project is to build the database of public domain software in biology and to distribute these software on-line as well as off-line. These computer software developed by people for people and are available free to potential users. The software collected on this site will be available on-line free for users via internet (e.g. FTP, Email Server, web browser ).
• 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.
• Slcview - Open source program which allows automated generation of high quality clustergrams and tree images from .cdt files.
• Software for Statistical Folding and Rational Design of Nucleic Acids - Sfold predicts probable RNA secondary structures, assesses target accessibility, and provides tools for the rational design of RNA-targeting nucleic acids. The web server version is free for academic use.
• STRING - Search for Tandem Repeats IN Genomes -- Includes C source code and examples.
• T-Coffee - T-Coffee is a multiple sequence alignment package using a novel algorithm, available for Unix, MS-DOS, and Mac OS X. Includes binaries, source, references, and documentation.
• 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 FASTA package of sequence comparison programs - William Pearson's package for fast sequence comparison
• The Sanger Centre: Software - Production software used at the Sanger Centre, physical mapping software, informatics and analysis software, and data formats
• VectorNTI - Commercial software suite for analysis and manipulation of DNA and protein sequences
• 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.
• 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."
• www.COMPBIO.net - Source code and research papers in computational biology. Includes downloadable Visualize molecule visualisation software which supports PDB and DAS files.
• XDigitize - A visualization software system for evaluation of hybridisation experiments.
• Search our Wiki for Bioinformatics Software - Find more information about this subject by clicking here