| Directory > Science > Biology > Bioinformatics > Software LucID Professional
Software for creating interactive keys for biology, taxonomy, medicine, and agriculture.
http://www.lucidcentral.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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BSML - Bioinformation Sequence Markup Language
Extensible language specification and container for bioinformatic data.
http://www.bsml.org/
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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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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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STRING
Search for Tandem Repeats IN Genomes -- Includes C source code and examples.
http://www.caspur.it/~castri/STRING/
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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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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/
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Paracel BLAST
Software for accelerated parallel BLAST searching
http://www.paracel.com/products/paracel_blast.html
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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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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
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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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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/
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AcaClone pDRAW32
Freeware DNA cloning, analysis and visualization software.
http://www.acaclone.com
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Array Genetics
Bioinformatics programs, including MendelBase.
http://www.arraygenetics.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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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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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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Slcview
Open source program which allows automated generation of high quality clustergrams and tree images
from .cdt files.
http://slcview.sourceforge.net
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VectorNTI
Commercial software suite for analysis and manipulation of DNA and protein sequences
http://www.informaxinc.com/solutions/vectornti/index.html
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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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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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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/
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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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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://physiologie.uni-ulm.de/kjr/Audrius/Sight/Index.html
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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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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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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/
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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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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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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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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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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/
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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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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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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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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/
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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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XDigitize
A visualization software system for evaluation of hybridisation experiments.
http://www.molgen.mpg.de/~xdigitise/
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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
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