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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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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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Phrap/Consed - http://www.phrap.org/
DNA sequence assembler and finishing tools from the UW Genome Center. |
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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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Generic Model Organism Database Construction Set - http://gmod.org/
Collection of interoperable open source software components for visualizing, annotation and managing data. |
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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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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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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://cbrg.inf.ethz.ch/Darwin/index.html - http://cbrg.inf.ethz.ch/Darwin/index.html
An interactive tool for peptide and nucleotide sequence analysis. |
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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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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.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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Unipro UGENE: Integrated Bioinformatics Tools - http://ugene.unipro.ru
Free cross-platform bioinformatics software package for DNA and protein sequence analysis. |
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Meta-MEME - http://metameme.sdsc.edu/
Software toolkit for building and using motif-based hidden Markov models of DNA and proteins - from the Univ. of California-San Diego. |
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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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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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Nano+Bio-Centre - http://nbc3.biologie.uni-kl.de
Offers a range of free software tools for annotating an entire genome, assembling sequences, gap closing and analysis of microarrays. |
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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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ARCiB -- Accessible Retired Computers in Biology - http://arcib.dowling.edu/
NSF supported project to make old computers accessible to new software in bioinformatics. Provides transitional and supplemental support, especially in structural biology, for software packages on various platforms. |
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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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Sequence Analysis - http://www.informagen.com/SA/
A freeware Java application that does many standard types of DNA and protein sequence analysis tasks. |
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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://www.lynnon.com - http://www.lynnon.com
Commercial software for DNA and Protein sequence analysis and manipulation. Available for Windows and Mac OS X. |
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http://www.ariadnegenomics.com/products/medscan.html - http://www.ariadnegenomics.com/products/medscan.html
Commercial Windows natural language processing software for the automated extraction of biological data from scientific literature. |
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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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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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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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MaGe (Magnifying Genomes) - Microbial genome Annotation System - http://www.genoscope.cns.fr/agc/mage/
The MaGe system offers a set of graphical interfaces which allow biologist to perform relevant expert annotation of microbial genomes. |
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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. |