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Sub-Categories in Software
Web Sites in Category 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.
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.
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.
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.
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.
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.
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.
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."
XDigitize - A visualization software system for evaluation of hybridisation experiments.
Related Categories:
Business > Healthcare > Computing > Software
Related Newsgroups:
bionet.software – Google
bionet.software.acedb – Google
bionet.software.gcg – Google
bionet.software.pc – Google
bionet.software.srs – Google
bionet.software.staden – Google
bionet.software.www – Google
bionet.software.x-plor – Google
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