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» 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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» 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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» 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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» 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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» Free FASTA/MultiFASTA converter tool
This tool will look for all FASTA files in the specified folder and will merge their content in a single file, generating a standard or custom MultiFASTA file. Just download the program and double click to run it. It does not need additional software/add-
http://www.dnabaser.com/download/FASTA-Converter/index.html
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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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» 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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» 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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» 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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» PeakTrace Basecaller
Software for base and quality scoring ABI DNA sequencing traces. Works with all ABI DNA sequencers including the ABI 377, ABI 310, ABI 3700, ABI 3100, ABI 3130 and ABI 3730.
https://www.nucleics.com/peaktrace/
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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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» Progeny Software
Supply pedigree drawing and genetic data management software for genetic research with a built-in customizable relational database.
http://www.progenygenetics.com
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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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» Seqool
Free Windows software tool for the analysis of DNA and RNA sequences. It includes several sequence statistics and a comprehensive set of signal search methods.
http://www.biossc.de/seqool/index.html
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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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» 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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