This category is for sites about stand-alone computer programs which process biological information such as genetic sequences.

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

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