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http://emboss.sourceforge.net/   » EMBOSS Open in a new browser window
   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/



http://adfconverter.sourceforge.net/   » ADF MAGE-ML Open in a new browser window
   Open source Java software for checking and conversion of MicroArray Array Design data file (ADF -Array Design File- MAGE-ML).
   http://adfconverter.sourceforge.net/

http://arcib.dowling.edu/   » ARCiB -- Accessible Retired Computers in Biology Open in a new browser window
   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/

http://www.timelogic.com/aks/index.html   » AlmaKnowledgeServer Open in a new browser window
   Text mining tool for genomics, proteomics platforms and drug discovery.
   http://www.timelogic.com/aks/index.html

http://bioinformatics.org/annhyb/   » AnnHyb Open in a new browser window
   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/

http://arrayanalysis.mbni.med.umich.edu/draw/   » Biological Concept Diagram Editor Open in a new browser window
   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/

http://www.dnabaser.com/download/DNA-Counter/index.html   » DNA Counter Open in a new browser window
   Small free Windows program to calculate nucleotides frequencies in DNA sequences.
   http://www.dnabaser.com/download/DNA-Counter/index.html

http://www.lynnon.com   » DNAMAN Open in a new browser window
   Commercial software for DNA and Protein sequence analysis and manipulation. Available for Windows and Mac OS X.
   http://www.lynnon.com

http://dnptrapper.sourceforge.net/   » DNPTrapper Open in a new browser window
   A Linux assembly editing and visualization tool specifically designed for manual analysis and finishing of repeated regions.
   http://dnptrapper.sourceforge.net/

http://cbrg.inf.ethz.ch/Darwin/index.html   » Darwin Open in a new browser window
   An interactive tool for peptide and nucleotide sequence analysis.
   http://cbrg.inf.ethz.ch/Darwin/index.html

http://www.ebi.ac.uk/expressionprofiler/   » Expression Profiler Open in a new browser window
   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/

http://www.dnabaser.com/download/FASTA-Converter/index.html   » FASTA Converter Open in a new browser window
   Free Windows tool for merging multiple FASTA files into a single FASTA file.
   http://www.dnabaser.com/download/FASTA-Converter/index.html

http://mozart.bio.neu.edu/friend/friend.html   » Friend Open in a new browser window
   An integrated multiple structure visualization and multiple sequence alignment application. Available for Windows, Linux.
   http://mozart.bio.neu.edu/friend/friend.html

http://www.bioafrica.net/GDElinux/index.html   » GDE Open in a new browser window
   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

http://www.genespotter.de   » Genespotter Open in a new browser window
   Commercial Windows software for analyzing biochip image data.
   http://www.genespotter.de

http://sourceforge.net/projects/genome-tools/   » Genome-tools Web Interface Open in a new browser window
   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/

http://gints.free.fr/english/eng_whatsAbout.htm   » Gints Open in a new browser window
   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_whatsAbout.htm

http://www.helsinki.fi/project/ritvos/GoCore/   » GoCore Open in a new browser window
   GoCore is a 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/

http://www.bioinfo-hr.org/inca   » INCA - INteractive Codon Analysis Open in a new browser window
   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

http://jaligner.sourceforge.net/   » JAligner Open in a new browser window
   Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment.
   http://jaligner.sourceforge.net/

http://bioinf.dms.med.uniroma1.it/JSTRING/   » JSTRING Open in a new browser window
   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/

http://www.korilog.com/products/improving-NCBI-BLAST.php   » KoriBlast Open in a new browser window
   Commercial graphical software for Blast searches.
   http://www.korilog.com/products/improving-NCBI-BLAST.php

http://www.ebi.ac.uk/~lenov/meltinghome.html   » MELTING Open in a new browser window
   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

http://chevreux.org/projects_mira.html   » MIRA Open in a new browser window
   A sequence assembly suite with SNP detection for "hard" projects.
   http://chevreux.org/projects_mira.html

http://www.genoscope.cns.fr/agc/mage/   » MaGe (Magnifying Genomes) - Microbial genome Annotation System Open in a new browser window
   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/

http://gel.ahabs.wisc.edu/mauve/   » Mauve Open in a new browser window
   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/

http://www.ariadnegenomics.com/products/medscan.html   » MedScan Open in a new browser window
   Commercial Windows natural language processing software for the automated extraction of biological data from scientific literature.
   http://www.ariadnegenomics.com/products/medscan.html

http://metameme.sdsc.edu/   » Meta-MEME Open in a new browser window
   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/

http://www.ncbi.nlm.nih.gov/BLAST/   » NCBI BLAST Open in a new browser window
   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/

http://nbc3.biologie.uni-kl.de   » Nano+Bio-Centre Open in a new browser window
   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

http://www.genome.washington.edu/UWGC/analysistools/Phred.cfm   » PHRED Open in a new browser window
   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

http://www.phrap.org/   » Phrap/Consed Open in a new browser window
   DNA sequence assembler and finishing tools from the UW Genome Center.
   http://www.phrap.org/

http://phylosort.sourceforge.net/   » PhyloSort Open in a new browser window
   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/

http://www.premierbiosoft.com/   » Premier Biosoft International Open in a new browser window
   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/

http://www.immunokin.com   » RGBG Analyzer Open in a new browser window
   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.
   http://www.immunokin.com

http://www.charite.de/bioinf/strap   » STRAP Open in a new browser window
   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

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

http://www.seqtools.dk   » Seqtools Open in a new browser window
   Commercial Windows software for batch handling and analysis of nucleotide and protein sequences.
   http://www.seqtools.dk

http://www.informagen.com/SA/   » Sequence Analysis Open in a new browser window
   A freeware Java application that does many standard types of DNA and protein sequence analysis tasks.
   http://www.informagen.com/SA/

http://sfold.wadsworth.org/index.pl   » Sfold Open in a new browser window
   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

http://www.bcgsc.ca/gc/bomge/sockeye/   » Sockeye Open in a new browser window
   3D visualisation platform for Comparative Genomics visualisation.
   http://www.bcgsc.ca/gc/bomge/sockeye/

http://tandem.bu.edu/trf/trf.html   » Tandem Repeats Finder Open in a new browser window
   Locates and displays tandem repeats in DNA sequences.
   http://tandem.bu.edu/trf/trf.html

http://www.arb-home.de   » The ARB Project Open in a new browser window
   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

http://blast.wustl.edu/   » WU-BLAST Open in a new browser window
   The Washington University improved version of BLAST. Free for academic users.
   http://blast.wustl.edu/

http://www.molgen.mpg.de/~xdigitise/   » XDigitize Open in a new browser window
   A Linux/Unix visualization software system for evaluation of hybridisation experiments.
   http://www.molgen.mpg.de/~xdigitise/

http://www.aborygen.com/downloads/biOpen/   » biOpen Open in a new browser window
   Commercial Mac OS X sequence analysis and structure visualization software.
   http://www.aborygen.com/downloads/biOpen/

http://bioinf.wehi.edu.au/limmaGUI/index.html   » limmaGUI Open in a new browser window
   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

http://www.acaclone.com   » pDRAW32 Open in a new browser window
   Freeware DNA cloning, analysis and visualization software.
   http://www.acaclone.com



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