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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.
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EMBOSS - 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.
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BioEdit - http://www.mbio.ncsu.edu/BioEdit/bioedit.html
Free Windows biological sequence alignment editor.
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HMMER - 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.
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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.
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Phrap/Consed - http://www.phrap.org/
DNA sequence assembler and finishing tools from the UW Genome Center.
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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.
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Generic Model Organism Database Construction Set - http://gmod.org/
Collection of interoperable open source software components for visualizing, annotation and managing data.
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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.
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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.
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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.
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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.
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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.
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sys-bio.org - http://sbw.kgi.edu/
Software for simulating metabolic, signal and genetic networks. Home of SBW, Jarnac, JDesigner and winSCAMP.
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MAFFT - 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.
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pDRAW32 - http://www.acaclone.com
Freeware DNA cloning, analysis and visualization software.
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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.
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SeWeR - http://bioinformatics.org/sewer/
An integrated portal for common web-based bioinformatics services. Built in Javascript as a standalone browser application.
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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.
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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.
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Tandem Repeats Finder - http://tandem.bu.edu/trf/trf.html
Locates and displays tandem repeats in DNA sequences.
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Seqtools - http://www.seqtools.dk
Commercial Windows software for batch handling and analysis of nucleotide and protein sequences.
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JAligner - http://jaligner.sourceforge.net/
Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment.
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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.
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MIRA - http://chevreux.org/projects_mira.html
A sequence assembly suite with SNP detection for "hard" projects.
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FASTA - http://www.ebi.ac.uk/Tools/fasta/
William Pearson's package for fast sequence comparison tools.
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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.
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Sockeye - http://www.bcgsc.ca/gc/bomge/sockeye/
3D visualisation platform for Comparative Genomics visualisation.
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BioMAJ - http://biomaj.genouest.org
Workflow engine dedicated to bio-data synchronization and processing.
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Darwin - http://cbrg.inf.ethz.ch/Darwin/index.html
An interactive tool for peptide and nucleotide sequence analysis.
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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.
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Unipro UGENE: Integrated Bioinformatics Tools - http://ugene.unipro.ru
Free cross-platform bioinformatics software package for DNA and protein sequence analysis.
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Sfold - 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.
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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.
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BioAfrica.net: Bioinformatics Software and Tools - http://www.bioafrica.net/bioinformaticstools.html
Bioinformatics software applications and tools developed by researchers. All the tools are open-source and freely available online.
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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.
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MELTING - 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.
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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.
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DNA Baser - http://www.dnabaser.com/
Sequence assembly software package including a free tool for merging multiple FASTA files into a single FASTA file.
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DNAMAN - http://www.lynnon.com
Commercial software for DNA and Protein sequence analysis and manipulation. Available for Windows and Mac OS X.
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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.
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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.
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MedScan - http://www.ariadnegenomics.com/products/medscan.html
Commercial Windows natural language processing software for the automated extraction of biological data from scientific literature.
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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.
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KoriBlast - http://www.korilog.com/products/improving-NCBI-BLAST.php
Commercial graphical software for Blast searches.
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CentiBiN: Centralities in Biological Networks - http://centibin.ipk-gatersleben.de/
Application for the calculation and visualization of centralities for biological networks.
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gsuffix - 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.
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Sequence Analysis - http://www.informagen.com/SA/
A freeware Java application that does many standard types of DNA and protein sequence analysis tasks.
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GeneRunner - http://www.generunner.net
A fairly old Windows sequence analysis tool for everyday lab use. Formerly a commercial product.
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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.
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XDigitize - http://www.molgen.mpg.de/~xdigitise/
A Linux/Unix visualization software system for evaluation of hybridisation experiments.
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DNPTrapper - http://dnptrapper.sourceforge.net/
A Linux assembly editing and visualization tool specifically designed for manual analysis and finishing of repeated regions.
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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.
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APBioKnoppix - http://opensource.nus.edu.sg/wiki/index.php/APBioKnoppix
Knoppix based bioinformatics software tools. Bootable from CD.
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Bioinformatics Tools in Haskell - http://malde.org/~ketil/
A bioinformatics library implemented in Haskell, including various utilities based on it.
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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.
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Genespotter - http://www.genespotter.de
Commercial Windows software for analyzing biochip image data.
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biOpen - http://www.lightwave-scientific.com/Resources/biOpen.pdf
Commercial Mac OS X sequence analysis and structure visualization software.
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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).
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Gints - 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.
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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.
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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.
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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.
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BioSoftwares - http://www.biosoftwares.com
Provides information on bioinformatic algorithms, tools and services.
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STRING - http://www.caspur.it/~castri/STRING/index.htm
Search for Tandem Repeats IN Genomes. Includes C source code and examples.
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MARBL - 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.
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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.
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HapEvolution - http://www.med.mun.ca/PTRG/What-We-Do/Research/PTRG-Research/HapEvolution.aspx
Java application which finds gene-gene interactions (multi chromosome) using SNP with interactive visualization.
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