XDigitize - A Linux/Unix visualization software system for evaluation of hybridisation experiments. 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. Phrap/Consed - DNA sequence assembler and finishing tools from the UW Genome Center. Darwin - An interactive tool for peptide and nucleotide sequence analysis. pDRAW32 - Freeware DNA cloning, analysis and visualization software. Sequence Analysis - A freeware Java application that does many standard types of DNA and protein sequence analysis tasks. 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 the ARB database can be accessed using Perl or C. 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. 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. limmaGUI - A graphical user interface for linear modelling of cDNA and oligonucleotide microarray data to identify differentially expressed genes. JAligner - Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment. EMBOSS - The European Molecular Biology Open Software Suite. An open source project started by the EMBnet community in order to replace proprietary systems like GCG. 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. MedScan - Commercial Windows natural language processing software for the automated extraction of biological data from scientific literature. Genespotter - Commercial Windows software for analyzing biochip image data. DNAMAN - Commercial software for DNA and Protein sequence analysis and manipulation. Available for Windows and Mac OS X. 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. MIRA - A sequence assembly suite with SNP detection for "hard" projects. Tandem Repeats Finder - Locates and displays tandem repeats in DNA sequences. 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. ADF MAGE-ML - Open source Java software for checking and conversion of MicroArray Array Design data file (ADF -Array Design File- MAGE-ML). Sockeye - 3D visualisation platform for Comparative Genomics visualisation. Seqtools - Commercial Windows software for batch handling and analysis of nucleotide and protein sequences. Gints - Object-oriented regulation network simulator written in Java. Includes downloadable software and documentation. The site is in French and English. SeWeR - An integrated portal for common web-based bioinformatics services. Built in Javascript as a standalone browser application. 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. DNPTrapper - A Linux assembly editing and visualization tool specifically designed for manual analysis and finishing of repeated regions. 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. FASTA - William Pearson's package for fast sequence comparison tools. BioEdit - Free Windows biological sequence alignment editor. MARBL - MARBL is a free (GPL) system to index the text portions of GenBank and associated NLM abstracts. Based on Mumps and the MDH. 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. BioMAJ - Workflow engine dedicated to bio-data synchronization and processing. biOpen - Commercial Mac OS X sequence analysis and structure visualization software. GeneRunner - A fairly old Windows sequence analysis tool for everyday lab use. Formerly a commercial product. Unipro UGENE: Integrated Bioinformatics Tools - Free cross-platform bioinformatics software package for DNA and protein sequence analysis. 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. CentiBiN: Centralities in Biological Networks - Application for the calculation and visualization of centralities for biological networks. Biochemfusion: Enabling Biochemformatics - Software for working with post-translationally or chemically modified peptides and proteins including proteins as both sequences and chemical structures. 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. GeneSifter - Provides complete systems for data-intensive genetic analysis applications like microarrays and next gen sequencing-based transcription. From Geospiza, Seattle, USA. DNA Baser Sequence Assembler - DNA sequence assembly software package capable of fully automated sequence assembly. CodonCode Corporation - Offers CodonCode Aligner, a DNA sequence assembly, sequence alignment, contig editing and mutation detection software for Windows and Mac OS X. Generic Model Organism Database Construction Set - Collection of interoperable open source software components for visualizing, annotation and managing data. BioAfrica.net: Bioinformatics Software and Tools - Bioinformatics software applications and tools developed by researchers. All the tools are open-source and freely available online. HapEvolution - Java application which finds gene-gene interactions (multi chromosome) using SNP with interactive visualization.