EMBOSS Save
The European Molecular Biology Open Software Suite. An open source project started by the EMBnet community in order to replace proprietary systems like GCG.
http://emboss.sourceforge.net/   

ADF MAGE-ML Save
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 Save
Knoppix based bioinformatics software tools. Bootable from CD.
http://www.apbionet.org/apbioknoppix/   

ARCiB -- Accessible Retired Computers in Biology Save
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 Save
Text mining tool for genomics, proteomics platforms and drug discovery.
http://aks.bioalma.com   

AnnHyb Save
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 Save
Free Windows biological sequence alignment editor.
http://www.mbio.ncsu.edu/BioEdit/bioe...   

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

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

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

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

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

Expression Profiler Save
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 Save
William Pearson's package for fast sequence comparison tools.
ftp://ftp.virginia.edu/pub/fasta   

FASTA Convertor Save
Free Windows tool for merging multiple FASTA files into a single FASTA file.
http://www.dnabaser.com/download/FAST...   

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

GDE Save
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/ind...   

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

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

Genome-tools Web Interface Save
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/genom...   

Gints Save
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_what...   

GoCore Save
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...   

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

JSTRING Save
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/JST...   

Keck Computational Systems Biology Software Save
Software for simulating metabolic, signal and genetic networks. Home of Jarnac, JDesigner and SCAMP.
http://sbw.kgi.edu/   

KoriBlast Save
Commercial graphical software for Blast searches.
http://www.korilog.com/products/impro...   

MAFFT Save
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/~kat...   

MARBL Save
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 Save
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/meltingho...   

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

MaGe (Magnifying Genomes) - Microbial genome Annotation System Save
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 Save
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 Save
Commercial Windows natural language processing software for the automated extraction of biological data from scientific literature.
http://www.ariadnegenomics.com/produc...   

Meta-MEME Save
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 Save
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 Save
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 Save
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...   

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

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

SeWeR Save
An integrated portal for common web-based bioinformatics services. Built in Javascript as a standalone browser application.
http://bioinformatics.org/sewer/   

Seqtools Save
Commercial Windows software for batch handling and analysis of nucleotide and protein sequences.
http://www.seqtools.dk   

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

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

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

The ARB Project Save
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   

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

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

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

limmaGUI Save
A graphical user interface for linear modelling of cDNA and oligonucleotide microarray data to identify differentially expressed genes.
http://bioinf.wehi.edu.au/limmaGUI/in...   

msa.cgb.ki.se Save
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 Save
Freeware DNA cloning, analysis and visualization software.
http://www.acaclone.com   

Forum - Usenet bionet.software
Forum - Usenet bionet.software.acedb
Forum - Usenet bionet.software.gcg
Forum - Usenet bionet.software.pc
Forum - Usenet bionet.software.srs
Forum - Usenet bionet.software.staden
Forum - Usenet bionet.software.www
Forum - Usenet bionet.software.x-plor

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