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Locus Technology, Inc
Colony management, supports creation and tracking of research animals: transgenic and congenic lines, knockouts and outbred strains.
http://www.locustechnology.com/
The BioCatalog
Software directory of general interest in molecular biology and genetics.
http://www.ebi.ac.uk/biocat/
MuStaR Sequence Variant Database Software
Designed to create a database of mutation loci, to make this information available to as many people as possible.
http://www.hgu.mrc.ac.uk/Softdata/Mustar/
TagSorter
Database application designed to simplify the collation, sorting, comparison and identification of SAGE tag sequences.
http://www.tagsorter.com
PopGen
Software that models population genetics with emphasis on genetic drift, selection, and migration.
http://cc.oulu.fi/~jaspi/popgen/popgen.htm
GeneSifter.Net
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/
R/qtl: A QTL Mapping Environment
Program for mapping quantitative trait loci in experimental crosses. Includes sample graphics and tutorial in pdf format.
http://www.biostat.jhsph.edu/~kbroman/qtl
Broad Institute
GeneHunter, MapMaker, Primer, and RHMapper documentation and free software, in UNIX and C source code.
http://www.broad.mit.edu/resources.html
LAMS
Freeware record keeping system designed for a breeding colony of transgenic mice. Includes program description, system requirements, and installation instructions.
http://www.hgu.mrc.ac.uk/Softdata/Lams/
Genetic Analysis Software
Extensive list of linkage, mapping and pedigree software with links for obtaining copies.
http://www.nslij-genetics.org/soft/
MapPop
Software for selective mapping and bin mapping by Daniel Brown and Todd Vision. WIN version, documentation and references are available here.
http://www.bio.unc.edu/faculty/vision/lab/mappop/
Progeny Software
Supply pedigree drawing and genetic data management software for genetic research with a built-in customizable relational database.
http://www.progeny2000.com
DRIFT
Graphically represents the effect of genetic drift on gene frequency of one or more populations for a single locus, two allele model in a closed population using stochastic simulation methods. The DOS program is free.
http://nitro.biosci.arizona.edu/zbook/general/gened.html
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.csa.ru/Inst/gorb_dep/inbios/genet/Urchin/u0maps.htm
Hands on Genetics
Instructional software for basic genetics, such as DNA, PCR, Mendel, Hardy-Weinberg, meiosis and computer simulations. Download WIN and MAC demos and order online.
http://www.handsongenetics.com
Advanced Genetics Wizard
Online program that calculates the distribution of offspring genotypes from dominant, codominant and recessive gene crosses, for up to 6 genes.
http://www.geneticswizard.com
Genetics Software
RASA 2.2 and other Mac software for phylogenetics, comparative genomics, and sequence analysis - from Penn State University.
http://evolution.genetics.washington.edu/phylip/software.pars.html
Istituto di Genetica Biochimica ed Evoluzionistica
Program that performs a permutation-based statistical test to detect genetic divergence among populations from DNA fingerprinting data . Downloadable source Fortran code, executable files and user manual .
http://www.igbe.pv.cnr.it/software.html
Big Bench Software
Database application for transgenic mouse colonies. Built-in networking capabilites, for both Mac and PC. Downloadable demo version.
http://www.bigbenchsoftware.com/
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/
STRand
Open-source program to automate or speed up the analysis of DNA fragment length polymorphism samples run on fluorescence based gels . Instructions for use and program download available .
http://www.vgl.ucdavis.edu/STRand
Genetic Linkage Analysis
Offers links and other resources for genetic analysis software from The Rockefeller University.
http://linkage.rockefeller.edu/
GeneticStudio
A complete suite of population genetic analysis programs for MAC. Includes plug-in modules.
http://www.umsl.edu/~biology/Dyer/GeneticStudio/
PowerSSR
Set of statistical methods for discrete genetic data analysis, designed especially for microsatellite data analysis. Includes downloadable versions for Windows and Linux.
http://statgen.ncsu.edu/statgen/soft_powerssr.html
The Darwin Manual
Guide and list of commands used to run this programming language. Library contains programs to compute pairwise alignments, phylogenetic trees, multiple sequence alignments, and to make secondary structure predictions.
http://www.inf.ethz.ch/personal/gonnet/DarwinManual/DarwinManual.html
Statistical Genetics Software
Collection of primarily Fortan programs for genetic analysis. Requires registration to download.
http://www.biomath.medsch.ucla.edu/faculty/klange/software.html
High Performance Computing and Informatics Office
US National Institutes of Health site with extensive genetic linkage analysis application resources on high performance computer systems. Formerly the Computational Methods and Algorithms Group.
http://hpcio.cit.nih.gov/
CircuSoft Instrumentation LLC
Transgenic mouse colony tracking and management software for Mac or Windows. Includes demo software and manuals.
http://www.circusoft.com/gmouse.html
Pegasys
Open source software for executing and integrating analyses of biological sequences. Includes documentation and installation instructions.
http://www.bioinformatics.ubc.ca/pegasys/
GENtle,
Application 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/
GeneX Virginia
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://genes.med.virginia.edu/
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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