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| Web Sites |
Alice Software
Database system to build and publish synonymised checklists of species. Species descriptions include pre-established fields and detailed descriptions employing any number of user-defined fields.
http://www.alicesoftware.com/
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Alternative Splice Site Predictor
ASSP predicts putative alternative exon isoform, cryptic, and constitutive splice sites of internal (coding) exons.
http://es.embnet.org/~mwang/assp.html
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BioConstructor Molecular Cloning Software
BioConstructor is a bioinformatics solution focussing on molecular cloning. Runs on Windows, Mac OS X, Linux.
http://www.bioconstructor.com
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Broad Institute Genetics Software
Offers a wide range of software for genome sequence analysis, genetic variation, linkage analysis, expression analysis, and PCR primer selection.
http://www.broad.mit.edu/tools/software.html
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CounterTrace II DNA Sequencing
Software and reagent for improving the quality and read length of DNA sequence traces collected on the ABI 3730 DNA sequencer.
http://www.nucleics.com/DNA_sequencing_tools/DNA-sequencing-software-countertrace.html
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CREME: Cis-REgulatory Module Explorer
Identifies modules of putative transcription factor binding sites that are specific to promoters of co-expressed human genes. Provides a resource for decoding microarray experiments.
http://creme.dcode.org/
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Gene Array Analyzer Software
Software for the efficient management, analysis and visualization of large amounts of gene expression data.
http://www.medinfopoli.polimi.it/GAAS/
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Gene Expression Open Source System
Open source database and analysis package used to archive and analyze expression data from gene chip experiments. Includes microarray center workflow management, and researcher tools to analyze final data.
https://biostat.virginia.edu/geoss/site/
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GeneSifter
Web-based microarray analysis system that combines data management and analytical functions with integrated, current gene annotation from public databases. Product overview in pdf format.
http://www.genesifter.net/web/
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Genetic Linkage Analysis
Offers links and other resources for genetic analysis software from the Rockefeller University.
http://linkage.rockefeller.edu/
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Genetic Network Maps as Java Applets
Genetic networks controlling development in Sea Urchin represented as Java applets. Formal scheme. Molecular interactions modelled as Petri Net.
http://www.bio.davidson.edu/courses/genomics/mirror/Urchin/u0maps.htm
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Genex Open Source Gene Expression Database
Genex is an open source database for storing, processing, and analyzing gene expression microarray data.It is intended for local installation by medium sized laboratories with some system administration support. No activity since 2003.
http://genex.sourceforge.net/
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GENtle
GPL software for viewing and editing DNA and amino acid sequences. Integrated alignment, PCR, BLAST searches, and shared databases. Windows version is available for download (English and German).
http://gentle.magnusmanske.de/
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Hands on Genetics
Instructional software for basic genetics, such as DNA, PCR, Mendel, Hardy-Weinberg, meiosis and computer simulations. Freeware for Mac and Windows.
http://www.handsongenetics.com
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MapMakerDrawer
Program that draws chromosome maps (as EMF files) using the output of MapMaker EXP. Delphi source code is freely available upon request. The software is available under the MIT licence.
http://www.emboss.co.nz/products.php?pid=2
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MuStaR Sequence Variant Database Software
Designed to create a database of mutation loci, to make this information available to as many people as possible. No longer being maintained.
http://www.hgu.mrc.ac.uk/Softdata/Mustar/
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Mutation Explorer
Software to automatically detect mutations from DNA sequence data, including homozygous, heterozygous, insertion and deletion.
http://www.softgenetics.com/mutationExplorer.html
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Pegasys
Open source software for executing and integrating analyses of biological sequences. Includes documentation and installation instructions.
http://www.bioinformatics.ubc.ca/pegasys/
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PyMoods
A software application for visualizing genomic data. Can be used to analyze and display relations between complete genomes, genomic fragments, proteins, ESTs, full length cDNAs, and gene expression data.
http://allometra.com/
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STRand
Open-source Windows program to automate or speed up the analysis of DNA fragment length polymorphism samples run on ABI3730, 3700 and 377 sequencers. Instructions for use and program download available.
http://www.vgl.ucdavis.edu/STRand
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Synopsis
Commercial Windows software for visualization and annotation of genomic data.
http://www.ananomouse.com/products/synopsis.asp
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TagSorter
Database application designed to simplify the collation, sorting, comparison and identification of SAGE tag sequences.
http://www.tagsorter.com
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The BioCatalog
Software directory of general interest in molecular biology and genetics. Not updated since 2000.
http://corba.ebi.ac.uk/Biocatalog/
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The Sequence Manipulation Suite
The Sequence Manipulation Suite is a collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. It is commonly used by molecular biologists, for teaching purposes, and for program and algorithm testing.
http://bioinformatics.org/sms2/
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