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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.
http://www.uk.embnet.org/Software/EMBOSS/
GeneRunner for Windows
A fairly old sequence analysis tool for everyday lab use. Formerly a commercial product - now "abandonware."
http://www.generunner.com
DNA-Star - Lasergene
Commercial sequence analysis and manipulation suite for Windows and Macintosh.
http://www.dnastar.com/
DARWIN
An interactive tool for peptide and nucleotide sequence analysis
http://cbrg.inf.ethz.ch/Darwin/index.html
VectorNTI
Commercial software suite for analysis and manipulation of DNA and protein sequences
http://www.informaxinc.com/solutions/vectornti/index.html
Slcview
Open source program which allows automated generation of high quality clustergrams and tree images from .cdt files.
http://slcview.sourceforge.net
PHRED - Base-Calling Software with Quality Information
A widely-used program for calling DNA sequence bases from sequencer trace files.
http://www.genome.washington.edu/UWGC/analysistools/Phred.cfm
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.
http://www.bioafrica.net/GDElinux/index.html
GeneticXchange
Software for life science discovery; enterprise-level data integration and desktop biologists.
http://www.geneticxchange.com/
Array Genetics
Bioinformatics programs, including MendelBase.
http://www.arraygenetics.com/
AG BIODV Software
Links to software developed by the AG BIODV group. Tools for consensus, alignment and definition. Both downloads and executables.
http://www.gsf.de/biodv/software.html
XDigitize
A visualization software system for evaluation of hybridisation experiments.
http://www.molgen.mpg.de/~xdigitise/
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.
http://www.PremierBiosoft.com
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.
http://metameme.sdsc.edu/
AcaClone pDRAW32
Freeware DNA cloning, analysis and visualization software.
http://www.acaclone.com
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.
http://www.cs.ucr.edu/~stelo/Verbumculus/
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.
http://www.informagen.com/SA/
Paracel BLAST
Software for accelerated parallel BLAST searching
http://www.paracel.com/products/paracel_blast.html
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 ).
http://imtech.res.in/pdsb/
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.
http://www.arb-home.de
STRING
Search for Tandem Repeats IN Genomes -- Includes C source code and examples.
http://www.caspur.it/~castri/STRING/
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.
http://sfold.wadsworth.org/index.pl
Gints
Object-oriented regulation network simulator written in Java. Includes downloadable software and documentation. The site is in French and English.
http://gints.free.Fr
BSML - Bioinformation Sequence Markup Language
Extensible language specification and container for bioinformatic data.
http://www.bsml.org/
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.
http://bioinformatics.org/annhyb/
LucID Professional
Software for creating interactive keys for biology, taxonomy, medicine, and agriculture.
http://www.lucidcentral.com/
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.
http://bioinformatics.org/jSight/
Metalifesocieties
Makes available various bioinformatics algorithms, which perform all essential tasks in sequence analysis and sequence-based predictions.
http://metalifesocieties.tripod.com/
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.
http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html
Linux Software Encyclopedia - Bioinformatics
Links to Bioinformatics software for Linux. From the Linux Software Encyclopedia.
http://stommel.tamu.edu/~baum/linuxlist/linuxlist/node9.html#biochemistry
Molecular Evolutionary Genetics Analysis (MEGA2) software
Provides free downloadable MEGA2 software for use in comparative sequence analysis of genetic data. Program for Win32 platforms.
http://megasoftware.net
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.
http://www.proBiosys.com
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
http://hmmer.wustl.edu/
The Sanger Centre: Software
Production software used at the Sanger Centre, physical mapping software, informatics and analysis software, and data formats
http://www.sanger.ac.uk/Software/
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.
http://www.pubcrawler.ie
Phred/Phrap/Consed System Home Page
basecaller / assembler / sequencer finisher and related tools from the UW Genome Center.
http://www.phrap.org/
Artemis: A DNA Sequence Viewer and Annotation Tool
Java program to display a DNA sequence, annotated with features, ORFs. Reads many input formats.
http://www.sanger.ac.uk/Software/Artemis/
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.
http://www.ncbi.nlm.nih.gov/BLAST/
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."
http://blast.wustl.edu/
The FASTA package of sequence comparison programs
William Pearson's package for fast sequence comparison
ftp://ftp.virginia.edu/pub/fasta
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.
http://www.genpakdna.com/genalysis/index.shtml
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