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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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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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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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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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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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http://biomaj.genouest.org - http://biomaj.genouest.org
Workflow engine dedicated to bio-data synchronization and processing. |
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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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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://gel.ahabs.wisc.edu/mauve/ - http://gel.ahabs.wisc.edu/mauve/
Free software for constructing global alignments of multiple rearranged genomes. The visualization environment displays sequence similarity profiles and annotated sequence features. |
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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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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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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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JAligner - http://jaligner.sourceforge.net/
Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment. |
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http://www.genome.washington.edu/UWGC/analysistools/Phred.cfm - http://www.genome.washington.edu/UWGC/analysistools/Phred.cfm
A widely-used program for base calling DNA sequencing trace files. Source code available and free for non-commercial users. |
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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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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://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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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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PhyloSort - http://phylosort.sourceforge.net/
A Java tool to sort phylogenetic trees by searching for user-specified subtrees that contain a monophyletic group of interest defined by operational taxonomic units. |
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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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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://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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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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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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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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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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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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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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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. |
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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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AlmaKnowledgeServer - http://www.timelogic.com/aks/index.html
Text mining tool for genomics, proteomics platforms and drug discovery. |
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Biological Concept Diagram Editor - http://arrayanalysis.mbni.med.umich.edu/draw/
A tool designed for efficient knowledge and data capture from electronic resources for sharing, mining and presentation purposes. |