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http://emboss.sourceforge.net/ - http://emboss.sourceforge.net/
The European Molecular Biology Open Software Suite. An open source project started by the EMBnet community in order to replace proprietary systems like GCG. |
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Phrap/Consed - http://www.phrap.org/
DNA sequence assembler and finishing tools from the UW Genome Center. |
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Premier Biosoft International - http://www.premierbiosoft.com/
Developers of software for real time PCR primer design, TaqMan, molecular beacons, SYBR green, FRET, DNA microarray analysis, restriction cloning, plasmid maps, gateway cloning, protein interaction network and functional genomics. |
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CodonCode Corporation - http://www.codoncode.com/
Offers CodonCode Aligner, a DNA sequence assembly, sequence alignment, contig editing and mutation detection software for Windows and Mac OS X. |
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sys-bio.org - http://sbw.kgi.edu/
Software for simulating metabolic, signal and genetic networks. Home of SBW, Jarnac, JDesigner and winSCAMP. |
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The ARB Project - http://www.arb-home.de
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. |
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Expression Profiler - http://www.ebi.ac.uk/expressionprofiler/
An open, extensible web-based collaborative platform for microarray gene expression, sequence and PPI data analysis, exposing distinct chainable components for clustering, pattern discovery, statistics, machine-learning algorithms and visualization. |
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Geneious - http://www.geneious.com
This research software is designed for biologists and not computer scientists. It combines all the major DNA and protein sequence analysis tools into one software solution. |
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http://www.charite.de/bioinf/strap - http://www.charite.de/bioinf/strap
Software supports the analysis of hundreds of proteins and integrates aa sequence, secondary structure, 3D-structure and genomic- and mRNA-sequence, and residue annotation. |
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http://bioinformatics.org/sewer/ - http://bioinformatics.org/sewer/
An integrated portal for common web-based bioinformatics services. Built in Javascript as a standalone browser application. |
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http://www.ebi.ac.uk/~lenov/meltinghome.html - http://www.ebi.ac.uk/~lenov/meltinghome.html
Computes, for a nucleic acid duplex, the enthalpy, the entropy and the melting temperature of the helix-coil transitions. |
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http://sfold.wadsworth.org/index.pl - http://sfold.wadsworth.org/index.pl
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. |
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NEXML: Phylogenetic Data in xml - http://www.nexml.org
Exchange standard for representing phylogenetic data, inspired by the commonly used NEXUS format but more robust and easier to process. |
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GeneSifter - http://www.genesifter.net
Provides complete systems for data-intensive genetic analysis applications like microarrays and next gen sequencing-based transcription. From Geospiza, Seattle, USA. |
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limmaGUI - http://bioinf.wehi.edu.au/limmaGUI/index.html
A graphical user interface for linear modelling of cDNA and oligonucleotide microarray data to identify differentially expressed genes. |
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http://mozart.bio.neu.edu/friend/friend.html - http://mozart.bio.neu.edu/friend/friend.html
An integrated multiple structure visualization and multiple sequence alignment application. Available for Windows, Linux. |
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INCA - INteractive Codon Analysis - http://www.bioinfo-hr.org/inca
Windows software that computes and charts codon and amino acid frequencies in whole genomes. Produces fully customizable scatter plots with the possibility to export graphics or text files for further analysis. Free for academic users. |
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http://bioinformatics.org/annhyb/ - http://bioinformatics.org/annhyb/
Free software for working with and managing nucleotide sequences in multiple formats. Features include sequence annotation, restriction analysis, pattern searching, retrieval from servers. Released under GNU Public Licence. |
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http://www.helsinki.fi/project/ritvos/GoCore/ - http://www.helsinki.fi/project/ritvos/GoCore/
GoCore is a free Excel based tool for protein sequence alignment, comparisons and functional predictions in a simple, visually appealing, manner. |
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http://bioinf.dms.med.uniroma1.it/JSTRING/ - http://bioinf.dms.med.uniroma1.it/JSTRING/
Java program for searching Tandem Repeats (TR) in a DNA sequence. It shows the results also in a graphical format. |
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Bioinformatics Tools in Haskell - http://malde.org/~ketil/
A bioinformatics library implemented in Haskell, including various utilities based on it. |
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http://www.bioafrica.net/GDElinux/index.html - http://www.bioafrica.net/GDElinux/index.html
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. |
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CentiBiN: Centralities in Biological Networks - http://centibin.ipk-gatersleben.de/
Application for the calculation and visualization of centralities for biological networks. |
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XDigitize - http://www.molgen.mpg.de/~xdigitise/
A Linux/Unix visualization software system for evaluation of hybridisation experiments. |
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GeneRunner - http://www.generunner.net
A fairly old Windows sequence analysis tool for everyday lab use. Formerly a commercial product. |
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Biomax BioXM Knowledge Management Environment - http://www.biomax.com/products/bioxm.php
Project-centered, distributed software platform that provides a central inventory of information and knowledge. Users create, manage and visualize scientific models as an extendible network of interrelated concepts. |
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http://gints.free.fr/english/eng_whatsAbout.htm - http://gints.free.fr/english/eng_whatsAbout.htm
Object-oriented regulation network simulator written in Java. Includes downloadable software and documentation. The site is in French and English. |
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ADF MAGE-ML - http://adfconverter.sourceforge.net/
Open source Java software for checking and conversion of MicroArray Array Design data file (ADF -Array Design File- MAGE-ML). |
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Biochemfusion: Enabling Biochemformatics - http://www.biochemfusion.com
Software for working with post-translationally or chemically modified peptides and proteins including proteins as both sequences and chemical structures. |
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Bioinformatics Software Tools - http://www.bio32.com
Provides access to a number of tools including biological databases, sequence allignment, analysis and manipulation tools and structural analysis tools. Also provides a glossary of bioinformatics terms. |
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RGBG Analyzer - http://www.immunokin.com
Commercial software to analyses the red, green, blue, and gray color values of user-selected areas of images in gif, tiff, bmp, jpeg format. Windows 2000 and XP. |
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Automated Codon Usage Analysis Software - http://www.bioinsilico.com/acua
ACUA is a freeware VB based interface for Insilico codon analysis. It provides nucleotide analysis, statistical codon analysis and positional nucleotide analysis. It presents the results in spreadsheets which can be utilized for further statistical analysis. |
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http://www.lightwave-scientific.com/Resources/biOpen.pdf - http://www.lightwave-scientific.com/Resources/biOpen.pdf
Commercial Mac OS X sequence analysis and structure visualization software. |
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http://www.caspur.it/~castri/STRING/index.htm - http://www.caspur.it/~castri/STRING/index.htm
Search for Tandem Repeats IN Genomes. Includes C source code and examples. |
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http://www.cs.uni.edu/~okane/source/MARBL/proc1.html - http://www.cs.uni.edu/~okane/source/MARBL/proc1.html
MARBL is a free (GPL) system to index the text portions of GenBank and associated NLM abstracts. Based on Mumps and the MDH. |