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Quantitative Genetics (26)

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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/
(Added: Mon Apr 04 2011 Hits: 0 Rating: 0.00 Votes: 0) Rate It Review It

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
(Added: Mon Apr 04 2011 Hits: 0 Rating: 0.00 Votes: 0) Rate It Review It

Binary State Pattern Clustering
BSPC is a method for pattern discovery in gene expression microarray data, that makes use of a perspective that interprets gene activity as being in two or more discrete functional states.
http://compbio.charite.de/index.php/BSPC.html
(Added: Mon Apr 04 2011 Hits: 0 Rating: 0.00 Votes: 0) Rate It Review It

BioConstructor Molecular Cloning Software
BioConstructor is a bioinformatics solution focussing on molecular cloning. Runs on Windows, Mac OS X, Linux.
http://www.bioconstructor.com
(Added: Mon Apr 04 2011 Hits: 0 Rating: 0.00 Votes: 0) Rate It Review It

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
(Added: Mon Apr 04 2011 Hits: 0 Rating: 0.00 Votes: 0) Rate It Review It

CellProfiler
Open source image analysis software designed for biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.
http://www.cellprofiler.org
(Added: Mon Apr 04 2011 Hits: 0 Rating: 0.00 Votes: 0) Rate It Review It

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
(Added: Mon Apr 04 2011 Hits: 0 Rating: 0.00 Votes: 0) Rate It Review It

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/
(Added: Mon Apr 04 2011 Hits: 0 Rating: 0.00 Votes: 0) Rate It Review It

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/
(Added: Mon Apr 04 2011 Hits: 0 Rating: 0.00 Votes: 0) Rate It Review It

Gene Expression Open Source System
Open source database and analysis package used to store and analyze gene expression data. Includes microarray center workflow management, and researcher tools to analyze final data.
http://va-genex.sourceforge.net/
(Added: Mon Apr 04 2011 Hits: 0 Rating: 0.00 Votes: 0) Rate It Review It

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/
(Added: Mon Apr 04 2011 Hits: 0 Rating: 0.00 Votes: 0) Rate It Review It

Genetic Linkage Analysis
Offers links and other resources for genetic analysis software from the Rockefeller University.
http://linkage.rockefeller.edu/
(Added: Mon Apr 04 2011 Hits: 0 Rating: 0.00 Votes: 0) Rate It Review It

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
(Added: Mon Apr 04 2011 Hits: 0 Rating: 0.00 Votes: 0) Rate It Review It

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/
(Added: Mon Apr 04 2011 Hits: 0 Rating: 0.00 Votes: 0) Rate It Review It

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/
(Added: Mon Apr 04 2011 Hits: 0 Rating: 0.00 Votes: 0) Rate It Review It

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
(Added: Mon Apr 04 2011 Hits: 0 Rating: 0.00 Votes: 0) Rate It Review It

HyPhy: Hypothesis Testing Using Phylogenies
Free multiplatform software package intended to perform maximum likelihood analyses of genetic sequence data.
http://www.hyphy.org
(Added: Mon Apr 04 2011 Hits: 0 Rating: 0.00 Votes: 0) Rate It Review It

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
(Added: Mon Apr 04 2011 Hits: 0 Rating: 0.00 Votes: 0) Rate It Review It

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/
(Added: Mon Apr 04 2011 Hits: 0 Rating: 0.00 Votes: 0) Rate It Review It

Mutation Explorer
Software to automatically detect mutations from DNA sequence data, including homozygous, heterozygous, insertion and deletion.
http://www.softgenetics.com/mutationExplorer.html
(Added: Mon Apr 04 2011 Hits: 0 Rating: 0.00 Votes: 0) Rate It Review It

OpenBiomind
OpenBiomind is an open source toolkit for analysis of gene expression, SNP and other biological datasets using advanced machine learning and pattern mining techniques, and includes traditional clustering, hybrid clustering, and other techniques.
http://code.google.com/p/openbiomind/
(Added: Mon Apr 04 2011 Hits: 0 Rating: 0.00 Votes: 0) Rate It Review It

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/
(Added: Mon Apr 04 2011 Hits: 0 Rating: 0.00 Votes: 0) Rate It Review It

Phenosystems
Software company developing user friendly tools for the molecular genetics community. Provides details of products, R and D collaborations and news.
http://www.phenosystems.com
(Added: Mon Apr 04 2011 Hits: 0 Rating: 0.00 Votes: 0) Rate It Review It

Progeny Software
Supply pedigree drawing and genetic data management software for genetic research with a built-in customizable relational database.
http://www.progenygenetics.com
(Added: Mon Apr 04 2011 Hits: 0 Rating: 0.00 Votes: 0) Rate It Review It

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/
(Added: Mon Apr 04 2011 Hits: 0 Rating: 0.00 Votes: 0) Rate It Review It

Random Genetic Optimization
Genetic algorithms are a new approach to modeling based on the evolution theory in biology and use concepts such as population, descendant, parents, mutations, chromosomes, genes, etc.
http://www.genoptim.narod.ru/ENG/
(Added: Mon Apr 04 2011 Hits: 0 Rating: 0.00 Votes: 0) Rate It Review It

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
(Added: Mon Apr 04 2011 Hits: 0 Rating: 0.00 Votes: 0) Rate It Review It

STRand
Open-source program, provided by Davis' Veterinary Genetics Lab at the University of California, to automate or speed up the analysis of DNA fragment length polymorphism samples.
http://www.vgl.ucdavis.edu/informatics/strand.php
(Added: Mon Apr 04 2011 Hits: 0 Rating: 0.00 Votes: 0) Rate It Review It

Synopsis
Commercial Windows software for visualization and annotation of genomic data.
http://www.ananomouse.com/products/synopsis.asp
(Added: Mon Apr 04 2011 Hits: 0 Rating: 0.00 Votes: 0) Rate It Review It

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/
(Added: Mon Apr 04 2011 Hits: 0 Rating: 0.00 Votes: 0) Rate It Review It

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