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Biotechnology Directory

Biotechnology: Bioinformatics Software

  • EMBOSS *Cool Site* - The European Molecular Biology Open Software Suite. An open source project started by the EMBnet community in order to replace proprieatry systems like GCG.
  • 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.
  • 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.
  • 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.
  • Artemis: A DNA Sequence Viewer and Annotation Tool - Java program to display a DNA sequence, annotated with features, ORFs. Reads many input formats.
  • Bio Informatic Bacterial Identification - Bibliographic site for management and alignment of bacteria and fungi sequences.
  • 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.
  • 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 - 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
  • JAligner - Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment.
  • limmaGUI - A graphical user interface for linear modelling of cDNA and oligonucleotide microarray data to identify differentially expressed genes.
  • Logical Depth - Accelerated sequence analysis tools for HMMsearch and Smith-Waterman.
  • LucID Professional - Software for creating interactive keys for biology, taxonomy, medicine, and agriculture.
  • Metalifesocieties - Makes available various bioinformatics algorithms, which perform all essential tasks in sequence analysis and sequence-based predictions.
  • 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.
  • 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.
  • 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.
  • The Sanger Centre: Software - Production software used at the Sanger Centre, physical mapping software, informatics and analysis software, and data formats
  • 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.
  • 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.
  • 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."
  • XDigitize - A visualization software system for evaluation of hybridisation experiments.
  • Linux Software Encyclopedia - Bioinformatics - Links to Bioinformatics software for Linux. From the Linux Software Encyclopedia.

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Modified by - 2005