:: DESCRIPTION
Evoker is a graphical tool for visualizing genotype intensity data in order to assess genotype calls as part of quality control procedures for genome-wide association studies.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Evoker: a visualization tool for genotype intensity data.
Morris JA, Randall JC, Maller JB and Barrett JC
Bioinformatics (Oxford, England) 2010;26;14;1786-7
:: DESCRIPTION
WHICHPARENTS is an application for determining the most likely parents of offspring, using mutlilocus genotype data. If parental mating history is known, this program also makes use of that information.
::DEVELOPER
Dennis Hedgecock, @ BODEGA MARINE LABORATORY
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
WHICHLOCI concerns these individual based population assignment methods but presents the method looking back on itself. Trial assignments with loci one at a time allows ranking of loci in terms of their efficiency for correct population assignment and conversely their propensity to cause false assignments. Subsequent trials with increasing numbers of loci determines what minimum number of which specific loci is required in order to attain defined power for population assignment.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2003 Jul 22;19(11):1436-8.
Which genetic loci have greater population assignment power?
Banks MA, Eichert W, Olsen JB.
:: DESCRIPTION
MGA-SIMULATE is a package of programs for simulation of genotypes and quantiative phenotyps given a pedigree structure, genetic map, alleleic frequencies and mode of inheritance for a quantitative trait.
::DEVELOPER
Laboratory of the Methods of Genetic Analysis , Institute of Cytology and Genetics, Novosibirsk, Russia.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
MouseDivGeno is a R package specifically designed to genotype the Mouse Diversity Genotyping Array, an Affymetrix mouse genotyping array similar to the human SNP 6.0. MouseDivGeno contains functions which allow you to perform genotyping, identify probe sets potentially harboring a new mutation (Variable INtensity Oligonucleotide or VINO, here we call it a vinotyping) and perform CNV analysis.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Genomics. 2012 Jan 19;13:34.
Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias.
Didion JP, Yang H, Sheppard K, Fu CP, McMillan L, de Villena FP, Churchill GA.
:: DESCRIPTION
HaploRec is a statistical haplotype reconstruction algorithm targeted for large-scale disease association studies. It is especially suitable for data sets with a large number of subjects and a large number of possibly sparsely located markers.
::DEVELOPER
Group of Data mining in genetics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Lauri Eronen, Floris Geerts, Hannu Toivonen.
HaploRec: Efficient and accurate large-scale reconstruction of haplotypes.
BMC Bioinformatics 7:542, 2006.
:: DESCRIPTION
HW-QuickCheck is a program for comparing genotypes with Hardy-Weinberg expectations. You paste a list a genotypes into a textbox and HW-QuickCheck tests the genotypes for equilibrium using a nice set of exact tests. It is designed to be used early in the genotyping process so that allelic dropout and null alleles can be detected as soon as possible.
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::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Kalinowski ST (In review)
HW-QuickCheck: an easy-to-use computer program for checking genotypes for agreement with Hardy-Weinberg expectations.
Molecular Ecology Notes. 2006, VOL 6; NUMBER 4, pages 974-979
:: DESCRIPTION
SGCaller is a Windows program that calls genotypes in sequencing traces.The software reads a collection of trace files in ABI or Staden (SCF) format, finds the variant position and tries to call the genotype for each, and presents them for the user to confirm and enhance the calling. SGCaller determines each file’s read direction from its name. After aligning sample traces to the reference, SGCaller calculates the total area under all four peaks for the base to be genotyped. Peak boundaries from the trace file are used; traces are not normalized to one another.
::DEVELOPER
Institute for Clinical Molecular Biology
:: SCREENSHOTS
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Manaster C, Valentonyte R, Teuber M, Zheng W, Schreiber S, Hampe J (2005).
SGCaller: A program to call and review genotypes measured by sequencing.
BioTechniques 38(4): 544-546
:: DESCRIPTION
Margarita infers genealogies from population genotype data and uses these to map disease loci.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Mapping trait loci by use of inferred ancestral recombination graphs.
Minichiello MJ and Durbin R
American journal of human genetics2006;79;5;910-22
:: DESCRIPTION
g2h.pl is a software to convert genotypes (in .ped format) to haplotypes
h2g.pl is a software to convert haplotypes to genotypes (in .ped format)
h2h.pl is a software to extract haplotypes for a subset of markers
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:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: MORE INFORMATION
