Web Directory

» ADF MAGE-ML
   Open source Java software for checking and conversion of MicroArray Array Design data file (ADF -Array Design File- MAGE-ML).
   http://adfconverter.sourceforge.net/

» APBioKnoppix
   Knoppix based bioinformatics software tools. Bootable from CD.
   http://opensource.nus.edu.sg/wiki/index.php/APBioKnoppix

» ARCiB -- Accessible Retired Computers in Biology
   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.
   http://arcib.dowling.edu/

» 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.
   http://bioinformatics.org/annhyb/

» Automated Codon Usage Analysis Software
   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 analys
   http://www.bioinsilico.com/acua

» BioAfrica.net: Bioinformatics Software and Tools
   Bioinformatics software applications and tools developed by researchers. All the tools are open-source and freely available online.
   http://www.bioafrica.net/bioinformaticstools.html

» BioEdit
   Free Windows biological sequence alignment editor.
   http://www.mbio.ncsu.edu/BioEdit/bioedit.html

» BioMAJ
   Workflow engine dedicated to bio-data synchronization and processing.
   http://biomaj.genouest.org

» BioSoftwares
   Provides information on bioinformatic algorithms, tools and services.
   http://www.biosoftwares.com

» Biochemfusion: Enabling Biochemformatics
   Software for working with post-translationally or chemically modified peptides and proteins including proteins as both sequences and chemical structures.
   http://www.biochemfusion.com

» Bioinformatics Tools in Haskell
   A bioinformatics library implemented in Haskell, including various utilities based on it.
   http://malde.org/~ketil/

» Biomax BioXM Knowledge Management Environment
   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.
   http://www.biomax.com/products/bioxm.php

» CentiBiN: Centralities in Biological Networks
   Application for the calculation and visualization of centralities for biological networks.
   http://centibin.ipk-gatersleben.de/

» CodonCode Corporation
   Offers CodonCode Aligner, a DNA sequence assembly, sequence alignment, contig editing and mutation detection software for Windows and Mac OS X.
   http://www.codoncode.com/

» Cytoscape
   Open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. It is also a general platform for complex network analysis and visualization
   http://www.cytoscape.org/

» DNA Baser
   Sequence assembly software package including a free tool for merging multiple FASTA files into a single FASTA file.
   http://www.dnabaser.com/

» DNAMAN
   Commercial software for DNA and Protein sequence analysis and manipulation. Available for Windows and Mac OS X.
   http://www.lynnon.com

» DNPTrapper
   A Linux assembly editing and visualization tool specifically designed for manual analysis and finishing of repeated regions.
   http://dnptrapper.sourceforge.net/

» Darwin
   An interactive tool for peptide and nucleotide sequence analysis.
   http://cbrg.inf.ethz.ch/Darwin/index.html

» Expression Profiler
   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.
   http://www.ebi.ac.uk/expressionprofiler/

» FASTA
   William Pearson's package for fast sequence comparison tools.
   http://www.ebi.ac.uk/Tools/fasta/

» GeneRunner
   A fairly old Windows sequence analysis tool for everyday lab use. Formerly a commercial product.
   http://www.generunner.net

» GeneSifter
   Provides complete systems for data-intensive genetic analysis applications like microarrays and next gen sequencing-based transcription. From Geospiza, Seattle, USA.
   http://www.genesifter.net

» Geneious
   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.
   http://www.geneious.com

» Generic Model Organism Database Construction Set
   Collection of interoperable open source software components for visualizing, annotation and managing data.
   http://gmod.org/

» Genespotter
   Commercial Windows software for analyzing biochip image data.
   http://www.genespotter.de

» Genome-tools Web Interface
   Genome-tools provides flexible tools and a simple API for genomic sequence processing on genomes published in the standard Genbank format.
   http://sourceforge.net/projects/genome-tools/

» 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/english/eng_whatsAbout.htm

» GoCore
   GoCore is a free Excel based tool for protein sequence alignment, comparisons and functional predictions in a simple, visually appealing, manner.
   http://www.helsinki.fi/project/ritvos/GoCore/

» HMMER
   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.
   http://hmmer.janelia.org/

» HapEvolution
   Java application which finds gene-gene interactions (multi chromosome) using SNP with interactive visualization.
   http://www.med.mun.ca/PTRG/What-We-Do/Research/PTRG-Research/HapEvolution.aspx

» INCA - INteractive Codon Analysis
   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.
   http://www.bioinfo-hr.org/inca

» JAligner
   Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment.
   http://jaligner.sourceforge.net/

» JSTRING
   Java program for searching Tandem Repeats (TR) in a DNA sequence. It shows the results also in a graphical format.
   http://bioinf.dms.med.uniroma1.it/JSTRING/

» KoriBlast
   Commercial graphical software for Blast searches.
   http://www.korilog.com/products/improving-NCBI-BLAST.php

» MAFFT
   Multiple sequence alignment program for Linux and other unix-like operating systems. Offers a range of multiple alignment strategies.
   http://align.bmr.kyushu-u.ac.jp/mafft/online/server/

» MARBL
   MARBL is a free (GPL) system to index the text portions of GenBank and associated NLM abstracts. Based on Mumps and the MDH.
   http://www.cs.uni.edu/~okane/source/MARBL/proc1.html

» MELTING
   Computes, for a nucleic acid duplex, the enthalpy, the entropy and the melting temperature of the helix-coil transitions.
   http://www.ebi.ac.uk/~lenov/meltinghome.html

» MIRA
   A sequence assembly suite with SNP detection for "hard" projects.
   http://chevreux.org/projects_mira.html

» MaGe (Magnifying Genomes) - Microbial genome Annotation System
   The MaGe system offers a set of graphical interfaces which allow biologist to perform relevant expert annotation of microbial genomes.
   http://www.genoscope.cns.fr/agc/mage/

» Mauve
   Free software for constructing global alignments of multiple rearranged genomes. The visualization environment displays sequence similarity profiles and annotated sequence features.
   http://gel.ahabs.wisc.edu/mauve/

» MedScan
   Commercial Windows natural language processing software for the automated extraction of biological data from scientific literature.
   http://www.ariadnegenomics.com/products/medscan.html

» Meta-MEME
   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/

» NEXML: Phylogenetic Data in xml
   Exchange standard for representing phylogenetic data, inspired by the commonly used NEXUS format but more robust and easier to process.
   http://www.nexml.org

» Nano+Bio-Centre
   Offers a range of free software tools for annotating an entire genome, assembling sequences, gap closing and analysis of microarrays.
   http://nbc3.biologie.uni-kl.de

» Phrap/Consed
   DNA sequence assembler and finishing tools from the UW Genome Center.
   http://www.phrap.org/

» PhyloSort
   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.
   http://phylosort.sourceforge.net/

» Premier Biosoft International
   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.
   http://www.premierbiosoft.com/

» RGBG Analyzer
   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.
   http://www.immunokin.com

» SMSD (Small Molecule Subgraph Detector)
   SMSD is a Java based software library for calculating Maximum Common Subgraph (MCS) between small molecules. This will aid finding resemblances between two molecules and is also used for screening drug-like compounds.
   http://www.ebi.ac.uk/thornton-srv/software/SMSD/

» 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.
   http://www.charite.de/bioinf/strap

» STRING
   Search for Tandem Repeats IN Genomes. Includes C source code and examples.
   http://www.caspur.it/~castri/STRING/index.htm

» SeWeR
   An integrated portal for common web-based bioinformatics services. Built in Javascript as a standalone browser application.
   http://bioinformatics.org/sewer/

» Seqtools
   Commercial Windows software for batch handling and analysis of nucleotide and protein sequences.
   http://www.seqtools.dk

» Sequence Analysis
   A freeware Java application that does many standard types of DNA and protein sequence analysis tasks.
   http://www.informagen.com/SA/

» Sockeye
   3D visualisation platform for Comparative Genomics visualisation.
   http://www.bcgsc.ca/gc/bomge/sockeye/

» Tandem Repeats Finder
   Locates and displays tandem repeats in DNA sequences.
   http://tandem.bu.edu/trf/trf.html

» 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
   http://www.arb-home.de

» Unipro UGENE: Integrated Bioinformatics Tools
   Free cross-platform bioinformatics software package for DNA and protein sequence analysis.
   http://ugene.unipro.ru

» XDigitize
   A Linux/Unix visualization software system for evaluation of hybridisation experiments.
   http://www.molgen.mpg.de/~xdigitise/

» biOpen
   Commercial Mac OS X sequence analysis and structure visualization software.
   http://www.lightwave-scientific.com/Resources/biOpen.pdf

» gsuffix
   C-language implementations of generalized suffix-based algorithms useful for searching for string patterns in sets of input strings and is released under the terms of the LGPL license.
   http://compbio.charite.de/index.php/gsuffix.html

» limmaGUI
   A graphical user interface for linear modelling of cDNA and oligonucleotide microarray data to identify differentially expressed genes.
   http://bioinf.wehi.edu.au/limmaGUI/index.html

» msa.cgb.ki.se
   Open source software developed by Timo Lassmann for multiple sequence alignment, including Kalign, Kalignvu and Mumsa.
   http://msa.sbc.su.se/cgi-bin/msa.cgi

» pDRAW32
   Freeware DNA cloning, analysis and visualization software.
   http://www.acaclone.com

» sys-bio.org
   Software for simulating metabolic, signal and genetic networks. Home of SBW, Jarnac, JDesigner and winSCAMP.
   http://sbw.kgi.edu/