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HMMER - http://hmmer.janelia.org/
Profiles protein sequence data using hidden Markov models of a statistical descriptions of a sequence family's consensus. HMMER is a freely distributable implementation of profile HMM software for protein sequence analysis. |
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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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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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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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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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MELTING - 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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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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MAFFT - http://align.bmr.kyushu-u.ac.jp/mafft/online/server/
Multiple sequence alignment program for linux and other unix-like operating systems. Offers a range of multiple alignment strategies. |
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msa.cgb.ki.se - http://msa.cgb.ki.se/cgi-bin/msa.cgi
Open source software developed by Timo Lassmann for multiple sequence alignment, including Kalign, Kalignvu and Mumsa. |
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pDRAW32 - http://www.acaclone.com
Freeware DNA cloning, analysis and visualization software. |
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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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JAligner - http://jaligner.sourceforge.net/
Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment. |
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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 structual biology, for software packages on various platforms. |
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Sfold - 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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BioMAJ - http://biomaj.genouest.org
Workflow engine dedicated to bio-data synchronization and processing. |
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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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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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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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Bioinformatics Tools in Haskell - http://malde.org/~ketil/
A bioinformatics library implemented in Haskell, including various utilities based on it. |
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DNPTrapper - http://dnptrapper.sourceforge.net/
A Linux assembly editing and visualization tool specifically designed for manual analysis and finishing of repeated regions. |
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KoriBlast - http://www.korilog.com/products/improving-NCBI-BLAST.php
Commercial graphical software for Blast searches. |
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Gints - 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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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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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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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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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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GDE - 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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biOpen - http://www.lightwave-scientific.com/Resources/biOpen.pdf
Commercial Mac OS X sequence analysis and structure visualization software. |
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MARBL - 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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APBioKnoppix - http://opensource.nus.edu.sg/wiki/index.php/APBioKnoppix
Knoppix based bioinformatics software tools. Bootable from CD. |
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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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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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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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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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FASTA Converter - http://www.dnabaser.com/download/FASTA-Converter/index.html
Free Windows tool for merging multiple FASTA files into a single FASTA file. |