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://www.apbionet.org/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 structual biology, for software packages on various platforms.
   http://arcib.dowling.edu/

AlmaKnowledgeServer
   Text mining tool for genomics, proteomics platforms and drug discovery.
   http://www.timelogic.com/aks/index.html

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/

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

Biological Concept Diagram Editor
   A tool designed for efficient knowledge and data capture from electronic resources for sharing, mining and presentation purposes.
   http://arrayanalysis.mbni.med.umich.edu/draw/

DNA Counter
   Small free Windows program to calculate nucleotides frequencies in DNA sequences.
   http://www.dnabaser.com/download/DNA-Counter/index.html

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

DNPTrapper
   An 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.
   ftp://ftp.virginia.edu/pub/fasta

FASTA Convertor
   Free Windows tool for merging multiple FASTA files into a single FASTA file.
   http://www.dnabaser.com/download/FASTA-Converter/index.html

Friend
   An integrated multiple structure visualization and multiple sequence alignment application. Avaliable for Windows, Linux
   http://mozart.bio.neu.edu/friend/friend.html

GDE
   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.
   http://www.bioafrica.net/GDElinux/index.html

GeneRunner
   A fairly old Windows sequence analysis tool for everyday lab use. Formerly a commercial product - now "abandonware."
   http://www.generunner.com

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/

GoCore
   GoCore is an 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.wustl.edu/

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

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://sidhe.cs.uni.edu/marbl.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/

NCBI BLAST
   BLAST (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases regardless of whether the query is protein or DNA.
   http://www.ncbi.nlm.nih.gov/BLAST/

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

PHRED
   A widely-used program for base calling DNA sequencing trace files. Source code available and free for non-commecial users.
   http://www.genome.washington.edu/UWGC/analysistools/Phred.cfm

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 & XP.
   http://www.immunokin.com

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/

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/

Sfold
   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.
   http://sfold.wadsworth.org/index.pl

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

WU-BLAST
   The Washington University improved version of BLAST. Free for academic users.
   http://blast.wustl.edu/

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.aborygen.com/downloads/biOpen/

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.cgb.ki.se/cgi-bin/msa.cgi

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