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Software (56)

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http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/
Editor's Pick EMBOSS Open in a new browser window Editor's Pick
   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/

Sites:

http://arcib.dowling.edu/
ARCiB -- Accessible Retired Computers in Biology Open in a new browser window
   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/
http://www.aborygen.com
AbOrygen : Intuitive bioinformatics Open in a new browser window
   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
http://www.acaclone.com
AcaClone pDRAW32 Open in a new browser window
   Freeware DNA cloning, analysis and visualization software.
   http://www.acaclone.com
http://bioinformatics.org/annhyb/
AnnHyb - Nucleotidic Sequence Manager Open in a new browser window
   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/
http://www.arraygenetics.com/product_overview.php3
Array Genetics Open in a new browser window
   Bioinformatics programs, including MendelBase.
   http://www.arraygenetics.com/product_overview.php3
http://www.sanger.ac.uk/Software/Artemis/
Artemis: A DNA Sequence Viewer and Annotation Tool Open in a new browser window
   Java program to display a DNA sequence, annotated with features, ORFs. Reads many input formats.
   http://www.sanger.ac.uk/Software/Artemis/
http://www.bsml.org/
BSML - Bioinformation Sequence Markup Language Open in a new browser window
   Extensible language specification and container for bioinformatic data.
   http://www.bsml.org/
http://pbil.univ-lyon1.fr/bibi/query.php
Bio Informatic Bacterial Identification Open in a new browser window
   Bibliographic site for management and alignment of bacteria and fungi sequences.
   http://pbil.univ-lyon1.fr/bibi/query.php
http://www.proBiosys.com
Computer Program for Polyphasic Taxonomy Analysis Open in a new browser window
   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
http://cbrg.inf.ethz.ch/Darwin/index.html
DARWIN Open in a new browser window
   An interactive tool for peptide and nucleotide sequence analysis
   http://cbrg.inf.ethz.ch/Darwin/index.html
http://www.dnastar.com/
DNA-Star - Lasergene Open in a new browser window
   Commercial sequence analysis and manipulation suite for Windows and Macintosh.
   http://www.dnastar.com/
http://www.bioafrica.net/GDElinux/index.html
GDE for Linux Open in a new browser window
   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
http://bioinformatics.upmc.edu/GE2/GEDA.html
Gene Expression Data Analysis web application Open in a new browser window
   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
http://www.generunner.com
GeneRunner for Windows Open in a new browser window
   A fairly old sequence analysis tool for everyday lab use. Formerly a commercial product - now "abandonware."
   http://www.generunner.com
http://www.geneticxchange.com/
GeneticXchange Open in a new browser window
   Software for life science discovery; enterprise-level data integration and desktop biologists.
   http://www.geneticxchange.com/
http://gints.free.Fr
Gints Open in a new browser window
   Object-oriented regulation network simulator written in Java. Includes downloadable software and documentation. The site is in French and English.
   http://gints.free.Fr
http://hmmer.wustl.edu/
HMMER - profile hidden Markov models for sequence analysis Open in a new browser window
   Sean Eddy's tools to build HMMs from multiple alignments, align sequences to HMMs, calculate e-scores, and other tools
   http://hmmer.wustl.edu/
http://jaligner.sourceforge.net/
JAligner Open in a new browser window
   Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment.
   http://jaligner.sourceforge.net/
http://stommel.tamu.edu/~baum/linuxlist/linuxlist/node9.html#biochemistry
Linux Software Encyclopedia - Bioinformatics Open in a new browser window
   Links to Bioinformatics software for Linux. From the Linux Software Encyclopedia.
   http://stommel.tamu.edu/~baum/linuxlist/linuxlist/node9.html#biochemistry
http://logicaldepth.com/
Logical Depth Open in a new browser window
   Accelerated sequence analysis tools for HMMsearch and Smith-Waterman.
   http://logicaldepth.com/
http://www.lucidcentral.com/
LucID Professional Open in a new browser window
   Software for creating interactive keys for biology, taxonomy, medicine, and agriculture.
   http://www.lucidcentral.com/
http://metameme.sdsc.edu/
Meta-MEME v2.0.1 Open in a new browser window
   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/
http://metalifesocieties.tripod.com/
Metalifesocieties Open in a new browser window
   Makes available various bioinformatics algorithms, which perform all essential tasks in sequence analysis and sequence-based predictions.
   http://metalifesocieties.tripod.com/
http://megasoftware.net
Molecular Evolutionary Genetics Analysis (MEGA2) software Open in a new browser window
   Provides free downloadable MEGA2 software for use in comparative sequence analysis of genetic data. Program for Win32 platforms.
   http://megasoftware.net
http://www.ncbi.nlm.nih.gov/BLAST/
NCBI BLAST Open in a new browser window
   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/
http://www.genome.washington.edu/UWGC/analysistools/Phred.cfm
PHRED - Base-Calling Software with Quality Information Open in a new browser window
   A widely-used program for calling DNA sequence bases from sequencer trace files.
   http://www.genome.washington.edu/UWGC/analysistools/Phred.cfm
http://www.phrap.org/
Phred/Phrap/Consed System Home Page Open in a new browser window
   basecaller / assembler / sequencer finisher and related tools from the UW Genome Center.
   http://www.phrap.org/
http://www.PremierBiosoft.com
Premier Biosoft International Open in a new browser window
   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
http://www.pubcrawler.ie
PubCrawler - An Update Alerting Service for PubMed and GenBank Open in a new browser window
   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
http://www.caspur.it/~castri/STRING/
STRING Open in a new browser window
   Search for Tandem Repeats IN Genomes -- Includes C source code and examples.
   http://www.caspur.it/~castri/STRING/
http://www.informagen.com/SA/
Sequence Analysis for Mac OS X Open in a new browser window
   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/
http://bioinformatics.org/jSight/
Sight Open in a new browser window
   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, s
   http://bioinformatics.org/jSight/
http://sfold.wadsworth.org/index.pl
Software for Statistical Folding and Rational Design of Nucleic Acids Open in a new browser window
   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
http://www.arb-home.de
The ARB Project Open in a new browser window
   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
   http://www.arb-home.de
ftp://ftp.virginia.edu/pub/fasta
The FASTA package of sequence comparison programs Open in a new browser window
   William Pearson's package for fast sequence comparison
   ftp://ftp.virginia.edu/pub/fasta
http://www.sanger.ac.uk/Software/
The Sanger Centre: Software Open in a new browser window
   Production software used at the Sanger Centre, physical mapping software, informatics and analysis software, and data formats
   http://www.sanger.ac.uk/Software/
http://www.cs.ucr.edu/~stelo/Verbumculus/
Verbumculus Genetic Sequence Analyzer Open in a new browser window
   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/
http://blast.wustl.edu/
WU-BLAST Archives Open in a new browser window
   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/
http://www.molgen.mpg.de/~xdigitise/
XDigitize Open in a new browser window
   A visualization software system for evaluation of hybridisation experiments.
   http://www.molgen.mpg.de/~xdigitise/
http://bioinf.wehi.edu.au/limmaGUI/index.html
limmaGUI Open in a new browser window
   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

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Last Updated: 2004-11-13 13:15:44