Software (Bioinformatics)

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XDigitize A visualization software system for evaluation of hybridisation experiments. http://www.molgen.mpg.de/~xdigitise/ The FASTA package of sequence comparison programs William Pearson's package for fast sequence comparison ftp://ftp.virginia.edu/pub/fasta GeneRunner for Windows A fairly old sequence analysis tool for everyday lab use. Formerly a commercial product - now "abandonware." http://www.generunner.com Gene Expression Data Analysis web application Normalization tests for differentially expressed genes, clustering, bootstrapping, leave-one-out validation, cross-fold validation, and links to external genomic databases. http://bioinformatics.upmc.edu/GE2/GEDA.html BSML - Bioinformation Sequence Markup Language Extensible language specification and container for bioinformatic data. http://www.bsml.org/ JAligner Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment. http://jaligner.sourceforge.net/ DARWIN An interactive tool for peptide and nucleotide sequence analysis http://cbrg.inf.ethz.ch/Darwin/index.html PHRED - Base-Calling Software with Quality Information A widely-used program for calling DNA sequence bases from sequencer trace files. http://www.genome.washington.edu/UWGC/analysistools/Phred.cfm AbOrygen : Intuitive bioinformatics AbOrygen develops the next generation of bioinformatics software with powerful new features that simplify and improve the research work of life scientists worldwide. http://www.aborygen.com Verbumculus Genetic Sequence Analyzer An interesting tool to discover and visualize over- or under-represented words in genetic sequences. Executable for Sparc-Solaris, Sparc-Intel or Linux-Intel. Also available as a Java applet. http://www.cs.ucr.edu/~stelo/Verbumculus/ Molecular Evolutionary Genetics Analysis (MEGA2) software Provides free downloadable MEGA2 software for use in comparative sequence analysis of genetic data. Program for Win32 platforms. http://megasoftware.net 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/ Software for Statistical Folding and Rational Design of Nucleic Acids 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 GDE for Linux 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 Phred/Phrap/Consed System Home Page basecaller / assembler / sequencer finisher and related tools from the UW Genome Center. http://www.phrap.org/ Sequence Analysis for Mac OS X A freeware Mac OS X application written in Java that does many standard types of DNA and protein sequence analysis tasks. http://www.informagen.com/SA/ HMMER - profile hidden Markov models for sequence analysis Sean Eddy's tools to build HMMs from multiple alignments, align sequences to HMMs, calculate e-scores, and other tools http://hmmer.wustl.edu/ EMBOSS The European Molecular Biology Open Software Suite. An open source project started by the EMBnet community in order to replace proprieatry systems like GCG. http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/ Logical Depth Accelerated sequence analysis tools for HMMsearch and Smith-Waterman. http://logicaldepth.com/ 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 AcaClone pDRAW32 Freeware DNA cloning, analysis and visualization software. http://www.acaclone.com Artemis: A DNA Sequence Viewer and Annotation Tool Java program to display a DNA sequence, annotated with features, ORFs. Reads many input formats. http://www.sanger.ac.uk/Software/Artemis/ Sight Extendable parallel system for automatic genome analysis. Software for analysing all potential genes in a defined genome region. Given two marker names, can output reports of genomic features between them. Features for converting between naming systems, s http://bioinformatics.org/jSight/ The Sanger Centre: Software Production software used at the Sanger Centre, physical mapping software, informatics and analysis software, and data formats http://www.sanger.ac.uk/Software/ DNA-Star - Lasergene Commercial sequence analysis and manipulation suite for Windows and Macintosh. http://www.dnastar.com/ Metalifesocieties Makes available various bioinformatics algorithms, which perform all essential tasks in sequence analysis and sequence-based predictions. http://metalifesocieties.tripod.com/ Computer Program for Polyphasic Taxonomy Analysis The proBiosys suite of programs compares phenetic, chemotaxonomic and nucleic acid sequence data. Algorithms for polyphasic taxonomy are available to construct Dendrograms, the suite is simple to use. http://www.proBiosys.com Premier Biosoft International Developers of software for real time PCR primer design, TaqMan, molecular beacons, DNA microarray analysis, drawing restriction plasmid maps, gateway cloning experiments, protein interaction network and functional genomics. http://www.PremierBiosoft.com 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/ WU-BLAST Archives WU-BLAST: The Washington University BLAST. "...faster at any sensitivity, more sensitive at any speed, the first BLAST with gapped alignments and statistics." http://blast.wustl.edu/ LucID Professional Software for creating interactive keys for biology, taxonomy, medicine, and agriculture. http://www.lucidcentral.com/ 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 http://www.arb-home.de Bio Informatic Bacterial Identification Bibliographic site for management and alignment of bacteria and fungi sequences. http://pbil.univ-lyon1.fr/bibi/query.php AnnHyb - Nucleotidic Sequence Manager Free software for working with and managing nucleotide sequences in multiple formats. Many features including sequence annotation, restriction analysis, pattern searching, retrieval from servers. Released under GNU Public Licence. http://bioinformatics.org/annhyb/ STRING Search for Tandem Repeats IN Genomes -- Includes C source code and examples. http://www.caspur.it/~castri/STRING/ Linux Software Encyclopedia - Bioinformatics Links to Bioinformatics software for Linux. From the Linux Software Encyclopedia. http://stommel.tamu.edu/~baum/linuxlist/linuxlist/node9.html#biochemistry PubCrawler - An Update Alerting Service for PubMed and GenBank Software and an online service for periodically performing predefined searches at NCBI, reporting new results by email or on the web. http://www.pubcrawler.ie Meta-MEME v2.0.1 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/ Array Genetics Bioinformatics programs, including MendelBase. http://www.arraygenetics.com/product_overview.php3 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 GeneticXchange Software for life science discovery; enterprise-level data integration and desktop biologists. http://www.geneticxchange.com/

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