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Genome-tools Web Interface -
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/ 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.charite.de/bioinf/strap SeWeR -
An integrated portal for common web-based bioinformatics services. Built in Javascript as a standalone browser application.
http://bioinformatics.org/sewer/ MaGe (Magnifying Genomes) - Microbial genome Annotation System -
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/ Seqtools -
Commercial Windows software for batch handling and analysis of nucleotide and protein sequences.
http://www.seqtools.dk FASTA Converter -
Free Windows tool for merging multiple FASTA files into a single FASTA file.
http://www.dnabaser.com/download/FASTA-Converter/index.html pDRAW32 -
Freeware DNA cloning, analysis and visualization software.
http://www.acaclone.com ARCiB -- Accessible Retired Computers in Biology -
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/ INCA - INteractive Codon Analysis -
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 Premier Biosoft International -
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/ XDigitize -
A Linux/Unix visualization software system for evaluation of hybridisation experiments.
http://www.molgen.mpg.de/~xdigitise/ ADF MAGE-ML -
Open source Java software for checking and conversion of MicroArray Array Design data file (ADF -Array Design File- MAGE-ML).
http://adfconverter.sourceforge.net/ PHRED -
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 The ARB Project -
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 Gints -
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 GoCore -
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/ Darwin -
An interactive tool for peptide and nucleotide sequence analysis.
http://cbrg.inf.ethz.ch/Darwin/index.html WU-BLAST -
The Washington University improved version of BLAST. Free for academic users.
http://blast.wustl.edu/ Tandem Repeats Finder -
Locates and displays tandem repeats in DNA sequences.
http://tandem.bu.edu/trf/trf.html Phrap/Consed -
DNA sequence assembler and finishing tools from the UW Genome Center.
http://www.phrap.org/ Sfold -
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 Genespotter -
Commercial Windows software for analyzing biochip image data.
http://www.genespotter.de MedScan -
Commercial Windows natural language processing software for the automated extraction of biological data from scientific literature.
http://www.ariadnegenomics.com/products/medscan.html Friend -
An integrated multiple structure visualization and multiple sequence alignment application. Available for Windows, Linux.
http://mozart.bio.neu.edu/friend/friend.html Sockeye -
3D visualisation platform for Comparative Genomics visualisation.
http://www.bcgsc.ca/gc/bomge/sockeye/ MELTING -
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 JAligner -
Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment.
http://jaligner.sourceforge.net/ GDE -
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 Nano+Bio-Centre -
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 Biological Concept Diagram Editor -
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/ JSTRING -
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/ PhyloSort -
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/ DNAMAN -
Commercial software for DNA and Protein sequence analysis and manipulation. Available for Windows and Mac OS X.
http://www.lynnon.com KoriBlast -
Commercial graphical software for Blast searches.
http://www.korilog.com/products/improving-NCBI-BLAST.php RGBG Analyzer -
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 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/annhyb/ limmaGUI -
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 NCBI 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.
http://www.ncbi.nlm.nih.gov/BLAST/ AlmaKnowledgeServer -
Text mining tool for genomics, proteomics platforms and drug discovery.
http://www.timelogic.com/aks/index.html DNA Counter -
Small free Windows program to calculate nucleotides frequencies in DNA sequences.
http://www.dnabaser.com/download/DNA-Counter/index.html Mauve -
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/ DNPTrapper -
A Linux assembly editing and visualization tool specifically designed for manual analysis and finishing of repeated regions.
http://dnptrapper.sourceforge.net/ MIRA -
A sequence assembly suite with SNP detection for "hard" projects.
http://chevreux.org/projects_mira.html Expression Profiler -
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/ Sequence Analysis -
A freeware Java application that does many standard types of DNA and protein sequence analysis tasks.
http://www.informagen.com/SA/ Meta-MEME -
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/
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