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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.
http://arcib.dowling.edu/ |
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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.
http://www.aborygen.com |
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AcaClone pDRAW32 - Freeware DNA cloning, analysis and visualization software.
http://www.acaclone.com |
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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/ |
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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/ |
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Bio Informatic Bacterial Identification - Bibliographic site for management and alignment of bacteria and fungi sequences.
http://pbil.univ-lyon1.fr/bibi/query.php |
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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 |
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DARWIN - An interactive tool for peptide and nucleotide sequence analysis
http://cbrg.inf.ethz.ch/Darwin/index.html |
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DNA-Star - Lasergene - Commercial sequence analysis and manipulation suite for Windows and Macintosh.
http://www.dnastar.com/ |
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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.rfcgr.mrc.ac.uk/Software/EMBOSS/ |
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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 |
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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.
http://bioinformatics.upmc.edu/GE2/GEDA.html |
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GeneRunner for Windows - A fairly old sequence analysis tool for everyday lab use. Formerly a commercial product - now "abandonware."
http://www.generunner.com |
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GeneticXchange - Software for life science discovery; enterprise-level data integration and desktop biologists.
http://www.geneticxchange.com/ |
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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 |
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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 |
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Logical Depth - Accelerated sequence analysis tools for HMMsearch and Smith-Waterman.
http://logicaldepth.com/ |
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Metalifesocieties - Makes available various bioinformatics algorithms, which perform all essential tasks in sequence analysis and sequence-based predictions.
http://metalifesocieties.tripod.com/ |
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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 |
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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 |
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Phred/Phrap/Consed System Home Page - basecaller / assembler / sequencer finisher and related tools from the UW Genome Center.
http://www.phrap.org/ |
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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 |
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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 |
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STRING - Search for Tandem Repeats IN Genomes -- Includes C source code and examples.
http://www.caspur.it/~castri/STRING/ |
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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/ |
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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/ |
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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 |
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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 |
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The FASTA package of sequence comparison programs - William Pearson's package for fast sequence comparison
ftp://ftp.virginia.edu/pub/fasta |
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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/ |
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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/ |
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XDigitize - A visualization software system for evaluation of hybridisation experiments.
http://www.molgen.mpg.de/~xdigitise/ |
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limmaGUI - A graphical user interface for linear modelling of cDNA and oligonucleotide microarray data to identify differentially expressed genes.
http://bioinf.wehi.edu.au/limmaGUI/index.html |
