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XDigitize ?
http://www.molgen.mpg.de/~xdigitise/
A Linux/Unix visualization software system for evaluation of hybridisation experiments.
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.
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.
HMMER ?
http://hmmer.wustl.edu/
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.
Phrap/Consed ?
http://www.phrap.org/
DNA sequence assembler and finishing tools from the UW Genome Center.
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.
WU-BLAST ?
http://blast.wustl.edu/
The Washington University improved version of BLAST. Free for academic users.
FASTA ?
ftp://ftp.virginia.edu/pub/fasta
William Pearson's package for fast sequence comparison tools.
GeneRunner ?
http://www.generunner.com
A fairly old Windows sequence analysis tool for everyday lab use. Formerly a commercial product - now "abandonware."
Darwin ?
http://cbrg.inf.ethz.ch/Darwin/index.html
An interactive tool for peptide and nucleotide sequence analysis.
PHRED ?
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-commecial users.
GDE ?
http://www.bioafrica.net/GDElinux/index.html
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.
pDRAW32 ?
http://www.acaclone.com
Freeware DNA cloning, analysis and visualization software.
Sequence Analysis ?
http://www.informagen.com/SA/
A freeware Java application that does many standard types of DNA and protein sequence analysis tasks.
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.
STRING ?
http://www.caspur.it/~castri/STRING/
Search for Tandem Repeats IN Genomes. Includes C source code and examples.
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.
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.
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 structual biology, for software packages on various platforms.
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.
JAligner ?
http://jaligner.sourceforge.net/
Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment.
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.
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.
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.
MedScan ?
http://www.ariadnegenomics.com/products/medscan.html
Commercial Windows natural language processing software for the automated extraction of biological data from scientific literature.
Genespotter ?
http://www.genespotter.de
Commercial Windows software for analyzing biochip image data.
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.
DNAMAN ?
http://www.lynnon.com
Commercial software for DNA and Protein sequence analysis and manipulation. Available for Windows and Mac OS X.
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 & XP.
MIRA ?
http://chevreux.org/projects_mira.html
A sequence assembly suite with SNP detection for "hard" projects.
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.
Tandem Repeats Finder ?
http://tandem.bu.edu/trf/trf.html
Locates and displays tandem repeats in DNA sequences.
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.
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.
GoCore ?
http://www.helsinki.fi/project/ritvos/GoCore/
GoCore is an free Excel based tool for protein sequence alignment, comparisons and functional predictions in a simple, visually appealing, manner.
APBioKnoppix ?
http://www.apbionet.org/apbioknoppix/
Knoppix based bioinformatics software tools. Bootable from CD.
biOpen ?
http://www.aborygen.com/downloads/biOpen/
Commercial Mac OS X sequence analysis and structure visualization software.
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).
BioEdit ?
http://www.mbio.ncsu.edu/BioEdit/bioedit.html
Free Windows biological sequence alignment editor.
Sockeye ?
http://www.bcgsc.ca/gc/bomge/sockeye/
3D visualisation platform for Comparative Genomics visualisation.
Seqtools ?
http://www.seqtools.dk
Commercial Windows software for batch handling and analysis of nucleotide and protein sequences.
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.
SeWeR ?
http://bioinformatics.org/sewer/
An integrated portal for common web-based bioinformatics services. Built in Javascript as a standalone browser application.
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.
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.
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.
DNPTrapper ?
http://dnptrapper.sourceforge.net/
An Linux assembly editing and visualization tool specifically designed for manual analysis and finishing of repeated regions.
Friend ?
http://mozart.bio.neu.edu/friend/friend.html
An integrated multiple structure visualization and multiple sequence alignment application. Avaliable for Windows, Linux
msa.cgb.ki.se ?
http://msa.cgb.ki.se/cgi-bin/msa.cgi
Open source software developed by Timo Lassmann for multiple sequence alignment, including Kalign, Kalignvu and Mumsa.
DNA Counter ?
http://www.dnabaser.com/download/DNA-Counter/index.html
Small free Windows program to calculate nucleotides frequencies in DNA sequences.
FASTA Convertor ?
http://www.dnabaser.com/download/FASTA-Converter/index.html
Free Windows tool for merging multiple FASTA files into a single FASTA file.
Biological Concept Diagram Editor ?
http://arrayanalysis.mbni.med.umich.edu/draw/
A tool designed for efficient knowledge and data capture from electronic resources for sharing, mining and presentation purposes.
MARBL ?
http://sidhe.cs.uni.edu/marbl.html
MARBL is a free (GPL) system to index the text portions of GenBank and associated NLM abstracts. Based on Mumps and the MDH.
KoriBlast ?
http://www.korilog.com/products/improving-NCBI-BLAST.php
Commercial graphical software for Blast searches.
AlmaKnowledgeServer ?
http://www.timelogic.com/aks/index.html
Text mining tool for genomics, proteomics platforms and drug discovery.
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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