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

APBioKnoppix - http://opensource.nus.edu.sg/wiki/index.php/APBioKnoppix Knoppix based bioinformatics software tools. Bootable from CD.

ARCiB -- Accessible Retired Computers in Biology - http://arcib.dowling.edu/ NSF supported project to make old computers accessible to new software in bioinformatics. Provides transitional and supplemental support, especially in structural biology, for software packages on various platforms.

Automated Codon Usage Analysis Software - http://www.bioinsilico.com/acua ACUA is a freeware VB based interface for Insilico codon analysis. It provides nucleotide analysis, statistical codon analysis and positional nucleotide analysis. It presents the results in spreadsheets which can be utilized for further statistical analysis.

Biochemfusion: Enabling Biochemformatics - http://www.biochemfusion.com Software for working with post-translationally or chemically modified peptides and proteins including proteins as both sequences and chemical structures.

Bioinformatics Software Tools - http://www.bio32.com Provides access to a number of tools including biological databases, sequence allignment, analysis and manipulation tools and structural analysis tools. Also provides a glossary of bioinformatics terms.

Bioinformatics Tools in Haskell - http://malde.org/~ketil/ A bioinformatics library implemented in Haskell, including various utilities based on it.

Biomax BioXM Knowledge Management Environment - http://www.biomax.com/products/bioxm.php Project-centered, distributed software platform that provides a central inventory of information and knowledge. Users create, manage and visualize scientific models as an extendible network of interrelated concepts.

CentiBiN: Centralities in Biological Networks - http://centibin.ipk-gatersleben.de/ Application for the calculation and visualization of centralities for biological networks.

CodonCode Corporation - http://www.codoncode.com/ Offers CodonCode Aligner, a DNA sequence assembly, sequence alignment, contig editing and mutation detection software for Windows and Mac OS X.

Cytoscape - http://www.cytoscape.org/ Open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. It is also a general platform for complex network analysis and visualization.

DNA Baser - http://www.dnabaser.com/ Sequence assembly software package including a free tool for merging multiple FASTA files into a single FASTA file.

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

Expression Profiler - http://www.ebi.ac.uk/expressionprofiler/ 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.

Geneious - http://www.geneious.com This research software is designed for biologists and not computer scientists. It combines all the major DNA and protein sequence analysis tools into one software solution.

Generic Model Organism Database Construction Set - http://gmod.org/ Collection of interoperable open source software components for visualizing, annotation and managing data.

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

GeneSifter - http://www.genesifter.net Provides complete systems for data-intensive genetic analysis applications like microarrays and next gen sequencing-based transcription. From Geospiza, Seattle, USA.

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

Genome-tools Web Interface - http://sourceforge.net/projects/genome-tools/ Genome-tools provides flexible tools and a simple API for genomic sequence processing on genomes published in the standard Genbank format.

http://align.bmr.kyushu-u.ac.jp/mafft/online/server/ - http://align.bmr.kyushu-u.ac.jp/mafft/online/server/ Multiple sequence alignment program for Linux and other unix-like operating systems. Offers a range of multiple alignment strategies.

http://bioinf.dms.med.uniroma1.it/JSTRING/ - http://bioinf.dms.med.uniroma1.it/JSTRING/ Java program for searching Tandem Repeats (TR) in a DNA sequence. It shows the results also in a graphical format.

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

http://biomaj.genouest.org - http://biomaj.genouest.org Workflow engine dedicated to bio-data synchronization and processing.

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

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

http://compbio.charite.de/index.php/gsuffix.html - http://compbio.charite.de/index.php/gsuffix.html C-language implementations of generalized suffix-based algorithms useful for searching for string patterns in sets of input strings and is released under the terms of the LGPL license.

http://emboss.sourceforge.net/ - http://emboss.sourceforge.net/ 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://gel.ahabs.wisc.edu/mauve/ - http://gel.ahabs.wisc.edu/mauve/ Free software for constructing global alignments of multiple rearranged genomes. The visualization environment displays sequence similarity profiles and annotated sequence features.

http://gints.free.fr/english/eng_whatsAbout.htm - http://gints.free.fr/english/eng_whatsAbout.htm Object-oriented regulation network simulator written in Java. Includes downloadable software and documentation. The site is in French and English.

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

http://sfold.wadsworth.org/index.pl - http://sfold.wadsworth.org/index.pl 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://www.acaclone.com - http://www.acaclone.com Freeware DNA cloning, analysis and visualization software.

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

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

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

http://www.charite.de/bioinf/strap - http://www.charite.de/bioinf/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.cs.uni.edu/~okane/source/MARBL/proc1.html - http://www.cs.uni.edu/~okane/source/MARBL/proc1.html MARBL is a free (GPL) system to index the text portions of GenBank and associated NLM abstracts. Based on Mumps and the MDH.

http://www.ebi.ac.uk/~lenov/meltinghome.html - http://www.ebi.ac.uk/~lenov/meltinghome.html Computes, for a nucleic acid duplex, the enthalpy, the entropy and the melting temperature of the helix-coil transitions.

http://www.ebi.ac.uk/Tools/fasta/ - http://www.ebi.ac.uk/Tools/fasta/ William Pearson's package for fast sequence comparison tools.

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

http://www.helsinki.fi/project/ritvos/GoCore/ - http://www.helsinki.fi/project/ritvos/GoCore/ GoCore is a free Excel based tool for protein sequence alignment, comparisons and functional predictions in a simple, visually appealing, manner.

http://www.lightwave-scientific.com/Resources/biOpen.pdf - http://www.lightwave-scientific.com/Resources/biOpen.pdf Commercial Mac OS X sequence analysis and structure visualization software.

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

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

INCA - INteractive Codon Analysis - http://www.bioinfo-hr.org/inca 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.

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

KoriBlast - http://www.korilog.com/products/improving-NCBI-BLAST.php Commercial graphical software for Blast searches.

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

MaGe (Magnifying Genomes) - Microbial genome Annotation System - http://www.genoscope.cns.fr/agc/mage/ The MaGe system offers a set of graphical interfaces which allow biologist to perform relevant expert annotation of microbial genomes.

Meta-MEME - http://metameme.sdsc.edu/ Software toolkit for building and using motif-based hidden Markov models of DNA and proteins - from the Univ. of California-San Diego.

msa.cgb.ki.se - http://msa.sbc.su.se/cgi-bin/msa.cgi Open source software developed by Timo Lassmann for multiple sequence alignment, including Kalign, Kalignvu and Mumsa.

Nano+Bio-Centre - http://nbc3.biologie.uni-kl.de Offers a range of free software tools for annotating an entire genome, assembling sequences, gap closing and analysis of microarrays.

NCBI BLAST - http://www.ncbi.nlm.nih.gov/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.

NEXML: Phylogenetic Data in xml - http://www.nexml.org Exchange standard for representing phylogenetic data, inspired by the commonly used NEXUS format but more robust and easier to process.

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

PhyloSort - http://phylosort.sourceforge.net/ 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.

Premier Biosoft International - http://www.premierbiosoft.com/ 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.

RGBG Analyzer - http://www.immunokin.com 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.

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

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

SMSD (Small Molecule Subgraph Detector) - http://www.ebi.ac.uk/thornton-srv/software/SMSD/ SMSD is a Java based software library for calculating Maximum Common Subgraph (MCS) between small molecules. This will aid finding resemblances between two molecules and is also used for screening drug-like compounds.

sys-bio.org - http://sbw.kgi.edu/ Software for simulating metabolic, signal and genetic networks. Home of SBW, Jarnac, JDesigner and winSCAMP.

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

The ARB Project - http://www.arb-home.de 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.

Unipro UGENE: Integrated Bioinformatics Tools - http://ugene.unipro.ru Free cross-platform bioinformatics software package for DNA and protein sequence analysis.

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

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

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