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Home / Science / Biology / Bioinformatics / Software
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- Science/ Biology/ Evolution/ Software@ (13)
- Science/ Biology/ Genetics/ Software@ (42)
- Science/ Biology/ Instruments and Supplies/ Software@ (23)
- Science/ Biology/ Taxonomy/ Software@ (45)
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Web Sites
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- AcaClone pDRAW32 - Freeware DNA cloning, analysis and visualisation software
medlem.spray.se/acaclone
- AG BIODV Software - Links to software developed by the AG BIODV group. Tools for consensus, alignment and definition. Both downloads and executables.
www.gsf.de/biodv/software.html
- 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.
annhyb.free.fr
- Artemis: A DNA Sequence Viewer and Annotation Tool - Java program to display a DNA sequence, annotated with features, ORFs. Reads many input formats.
www.sanger.ac.uk/Software/Artemis
- BioAfrica - genetic data environment (GDE) for Linux download - An integrated linux environment for bioinformatics and evolutionary analysis based on the Genetic Data Environment (GDE)
www.bioafrica.net/GDElinux
- 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.
www.proBiosys.com
- DARWIN - An interactive tool for peptide and nucleotide sequence analysis
cbrg.inf.ethz.ch/Darwin/index.html
- DNA-Star - Lasergene - Commercial sequence analysis and manipulation suite for Windows and Macintosh.
www.dnastar.com
- Genalysis Genome Analysis Toolkit - Commercial tool for comparing whole genomes or large genetic sequences. Outputs lists of matches and dot-plots and supports web-based BLAST searches.
www.genpakdna.com/genalysis/index.shtml
- GeneRunner for Windows - A fairly old but still very usefull sequence analysis tool for everyday lab use. Formerly a commercial product - now "abandonware"
www.generunner.com
- 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
hmmer.wustl.edu
- Linux Software Encyclopedia - Bioinformatics - Links to Bioinformatics software for Linux. From the Linux Software Encyclopedia.
stommel.tamu.edu/~baum/linuxlist/linuxlist/node9.html#biochemistry
- 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.
metameme.sdsc.edu
- Molecular Evolutionary Genetics Analysis (MEGA2) software - Provides free downloadable MEGA2 software for use in comparative sequence analysis of genetic data. Program for Win32 platforms.
megasoftware.net
- 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.
www.ncbi.nlm.nih.gov/BLAST
- PHRED - Base-Calling Software with Quality Information - A widely-used program for calling DNA sequence bases from sequencer trace files.
www.genome.washington.edu/UWGC/analysistools/Phred.cfm
- Phred/Phrap/Consed System Home Page - basecaller / assembler / sequencer finisher and related tools from the UW Genome Center.
www.phrap.org
- PREMIER Biosoft International - Makers of Primer Premier PCR primer design software, Plasmid Premier plasmid vector map drawing software, and Array Designer cDNA microarray software.
www.PremierBiosoft.com
- 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.
www.pubcrawler.ie
- 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. Has features for converting between naming systems, sequence retrieval, E-PCR, gene prediction, similarity search, protein pattern search, report formatting etc. Written in Java.
physiologie.uni-ulm.de/kjr/Audrius/Sight/Index.html
- slcview - slcview is an open source program which allows automated generation of high quality clustergrams and tree images from .cdt files.
slcview.sourceforge.net
- Software for Life Science Discovery - geneticXchange provides powerful software for enterprise-level data integration and desktop biologists.
www.geneticxchange.com/Home.html
- The FASTA package of sequence comparison programs - William Pearson's package for fast sequence comparison
ftp://ftp.virginia.edu/pub/fasta
- The Sanger Centre: Software - Production software used at the Sanger Centre, physical mapping software, informatics and analysis software, and data formats
www.sanger.ac.uk/Software
- VectorNTI - Commercial software suite for analysis and manipulation of DNA and protein sequences
www.informaxinc.com/solutions/vectornti/index.html
- 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.
www.cs.purdue.edu/homes/stelo/Verbumculus
- 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."
blast.wustl.edu
- www.COMPBIO.net - Source code and research papers in computational biology. Includes downloadable Visualize molecule visualisation software which supports PDB and DAS files.
www.compbio.net/index.html
- XDigitize - A visualization software system for evaluation of hybridisation experiments.
www.molgen.mpg.de/~xdigitise
- 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.
www.uk.embnet.org/Software/EMBOSS
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