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/

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

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

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/

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

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

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

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

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

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/

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

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

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

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

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/

biOpen
- Commercial Mac OS X sequence analysis and structure visualization software.
- http://www.aborygen.com/downloads/biOpen/

APBioKnoppix
- Knoppix based bioinformatics software tools. Bootable from CD.
- http://www.apbionet.org/apbioknoppix/

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/

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

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/

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

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

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

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

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/

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

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

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

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/

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

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

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/

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/

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

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

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

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

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

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

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

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

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

FASTA
- William Pearson's package for fast sequence comparison tools.
- ftp://ftp.virginia.edu/pub/fasta

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

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

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/

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/

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/

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