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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://math-cs.cns.uni.edu/~okane/cgi-bin/...
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.ht...
APBioKnoppix
Knoppix based bioinformatics software tools. Bootable from CD.
http://www.apbionet.org/apbioknoppix/
Sockeye
3D visualisation platform for Comparative Genomics visualisation.
http://www.bcgsc.ca/gc/bomge/sockeye/
STRING
Search for Tandem Repeats IN Genomes. Includes C source code and examples.
http://www.caspur.it/~castri/STRING/
HMMER
Sean Eddy's lab, present profile hidden Markov models for biological sequence analysis, a tool used to build HMMs from multiple alignments, and calculate e-scores.
http://hmmer.wustl.edu/
Seqtools
Commercial Windows software for batch handling and analysis of nucleotide and protein sequences.
http://www.seqtools.dk
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/
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/GoCo...
MedScan
Commercial Windows natural language processing software for the automated extraction of biological data from scientific literature.
http://www.ariadnegenomics.com/products/me...
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://aks.bioalma.com
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/
DNPTrapper
An Linux assembly editing and visualization tool specifically designed for manual analysis and finishing of repeated regions.
http://dnptrapper.sourceforge.net/
WU-BLAST
The Washington University improved version of BLAST. Free for academic users.
http://blast.wustl.edu/
FASTA
William Pearson's package for fast sequence comparison tools.
ftp://ftp.virginia.edu/pub/fasta
BLAST
NCBI's sequence similarity search tool designed to support analysis of nucleotide and protein databases.
http://www.ncbi.nlm.nih.gov/BLAST/
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-too...
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
Meta-MEME v2.0.1
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/
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.ht...
GeneRunner
A fairly old Windows sequence analysis tool for everyday lab use. Formerly a commercial product - now "abandonware."
http://www.generunner.com
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/
DNAMAN
Commercial software for DNA and Protein sequence analysis and manipulation. Available for Windows and Mac OS X.
http://www.lynnon.com
Tandem Repeats Finder
Locates and displays tandem repeats in DNA sequences.
http://tandem.bu.edu/trf/trf.html
XDigitize
A Linux/Unix visualization software system for evaluation of hybridisation experiments.
http://www.molgen.mpg.de/~xdigitise/
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/
pDRAW32
Freeware DNA cloning, analysis and visualization software.
http://www.acaclone.com
Keck Computational Systems Biology Software
Software for simulating metabolic, signal and genetic networks. Home of Jarnac, JDesigner and SCAMP.
http://sbw.kgi.edu/
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_whatsAbou...
Darwin
An interactive tool for peptide and nucleotide sequence analysis.
http://cbrg.inf.ethz.ch/Darwin/index.html
Genespotter
Commercial Windows software for analyzing biochip image data.
http://www.genespotter.de
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/
Sequence Analysis
A freeware Java application that does many standard types of DNA and protein sequence analysis tasks.
http://www.informagen.com/SA/
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
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
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
SeWeR
An integrated portal for common web-based bioinformatics services. Built in Javascript as a standalone browser application.
http://bioinformatics.org/sewer/
biOpen
Commercial Mac OS X sequence analysis and structure visualization software.
http://www.aborygen.com/downloads/biOpen/
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.
http://www.arb-home.de
MAFFT
Multiple sequence alignment program for linux and other unix-like operating systems. Offers a range of multiple alignment strategies.
http://www.biophys.kyoto-u.ac.jp/~katoh/pr...
MIRA
A sequence assembly suite with SNP detection for "hard" projects.
http://chevreux.org/projects_mira.html
Phrap/Consed
DNA sequence assembler and finishing tools from the UW Genome Center.
http://www.phrap.org/
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
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
Open source Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment.
http://jaligner.sourceforge.net/
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/anal...
BioEdit
Free Windows biological sequence alignment editor.
http://www.mbio.ncsu.edu/BioEdit/bioedit.h...
Friend
An integrated multiple structure visualization and multiple sequence alignment application. Avaliable for Windows, Linux
http://mozart.bio.neu.edu/friend/friend.ht...
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/
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.h...
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2006