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software
Science, Biology, Bioinformatics, Software
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Editor's Picks:
 - The European Molecular Biology Open Software Suite. An open source project started by the EMBnet community in order to replace proprieatry systems like GCG.
- A visualization software system for evaluation of hybridisation experiments.
- Software for creating interactive keys for biology, taxonomy, medicine, and agriculture.
- Software and an online service for periodically performing predefined searches at NCBI, reporting new results by email or on the web.
- Accelerated sequence analysis tools for HMMsearch and Smith-Waterman.
- 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.
- 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.
- 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.
- 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.
- A graphical user interface for linear modelling of cDNA and oligonucleotide microarray data to identify differentially expressed genes.
- 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
- Links to Bioinformatics software for Linux. From the Linux Software Encyclopedia.
- basecaller / assembler / sequencer finisher and related tools from the UW Genome Center.
- A widely-used program for calling DNA sequence bases from sequencer trace files.
- Object-oriented regulation network simulator written in Java. Includes downloadable software and documentation. The site is in French and English.
- 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
- Bibliographic site for management and alignment of bacteria and fungi sequences.
- Java program to display a DNA sequence, annotated with features, ORFs. Reads many input formats.
- Software for life science discovery; enterprise-level data integration and desktop biologists.
- 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.
- A freeware Mac OS X application written in Java that does many standard types of DNA and protein sequence analysis tasks.
- A fairly old sequence analysis tool for everyday lab use. Formerly a commercial product - now "abandonware."
- Normalization tests for differentially expressed genes, clustering, bootstrapping, leave-one-out validation, cross-fold validation, and links to external genomic databases.
- William Pearson's package for fast sequence comparison
- Provides free downloadable MEGA2 software for use in comparative sequence analysis of genetic data. Program for Win32 platforms.
- 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: The Washington University BLAST. "...faster at any sensitivity, more sensitive at any speed, the first BLAST with gapped alignments and statistics."
- An interactive tool for peptide and nucleotide sequence analysis
- Sean Eddy's tools to build HMMs from multiple alignments, align sequences to HMMs, calculate e-scores, and other tools
- Production software used at the Sanger Centre, physical mapping software, informatics and analysis software, and data formats
- Search for Tandem Repeats IN Genomes -- Includes C source code and examples.
- AbOrygen develops the next generation of bioinformatics software with powerful new features that simplify and improve the research work of life scientists worldwide.
- 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.
- Software toolkit for building and using motif-based hidden Markov models of DNA and proteins - from the Univ. of California-San Diego.
- Commercial sequence analysis and manipulation suite for Windows and Macintosh.
- Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment.
- 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.
- Freeware DNA cloning, analysis and visualization software.
- Extensible language specification and container for bioinformatic data.
- Bioinformatics programs, including MendelBase.
- Makes available various bioinformatics algorithms, which perform all essential tasks in sequence analysis and sequence-based predictions.
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