Genstat has a suite of procedures for statistical genetics. Several of these make use of Genstat’s REML facilities to estimate QTLs from single environment, multi-environment and multi-trait trials.
DQMAP |
displays a genetic map |
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DQMKSCORES |
plots a grid of marker scores for genotypes and indicates missing data |
DQMQTLSCAN |
plots the results of a genome-wide scan for QTL effects in multi-environment trials |
DQRECOMBINATIONS |
plots a matrix of recombination frequencies between markers |
DQSQTLSCAN |
plots the results of a genome-wide scan for QTL effects in single-environment trials |
GPREDICTION |
produces genomic predictions (breeding values) using phenotypic and molecular marker information |
QBESTGENOTYPES |
sorts individuals of a segregating population by their genetic similarity with a target genotype, using the identity by descent (IBD) information at QTL positions |
QCANDIDATES |
selects QTLs on the basis of a test statistic profile along the genome |
QDESCRIBE |
prints summary statistics of genotypes |
QEIGENANALYSIS |
uses principal components analysis and the Tracy-Widom statistic to find the number of significant principal components to represent a set of variables |
QEXPORT |
exports genotypic data for QTL analysis |
QFLAPJACK |
creates a Flapjack project file from genotypic and phenotypic data |
QGSELECT |
obtains a representative selection of genotypes by means of genetic distance sampling or genetic distance optimization |
QIBDPROBABILITIES |
reads molecular marker data and calculates IBD probabilities |
QIMPORT |
imports genotypic and phenotypic data for QTL analysis |
QKINSHIPMATRIX |
forms a kinship matrix from molecular markers |
QLDDECAY |
estimates linkage disequilibrium (LD) decay along a chromosome |
QLINKAGEGROUPS |
forms linkage groups using marker data from experimental populations |
QMAP |
constructs genetic linkage maps using marker data from experimental populations |
QMASSOCIATION |
performs multi-environment marker-trait association analysis in a genetically diverse population using bi-allelic and multi-allelic markers |
QMATCH |
matches different data structures to be used in QTL estimation |
QMBACKSELECT |
performs a QTL backward selection for loci in multi-environment trials or multiple populations |
QMESTIMATE |
calculates QTL effects in multi-environment trials or multiple populations |
QMKDIAGNOSTICS |
generates descriptive statistics and diagnostic plots of molecular marker data |
QMKRECODE |
recodes marker scores into separate alleles |
QMKSELECT |
obtains a representative selection of markers by means of genetic distance sampling or genetic distance optimization |
QMQTLSCAN |
performs a genome-wide scan for QTL effects (Simple and Composite Mapping) in multi-environment trials or multiple populations |
QMTBACKSELECT |
performs a QTL backward selection for loci in multi-trait trials |
QMTESTIMATE |
calculates QTL effects in multi-trait trials |
QMTQTLSCAN |
performs a genome-wide scan for QTL effects (Simple and Composite Interval Mapping) in multi-trait trials |
QMVAF |
calculates percentage variance accounted for by QTL effects in a multi-environment analysis |
QMVESTIMATE |
replaces missing molecular marker scores using conditional genotypic probabilities |
QMVREPLACE |
replaces missing marker scores with the mode scores of the most similar genotypes |
QRECOMBINATIONS |
calculates the expected numbers of recombinations and the recombination frequencies between markers |
QREPORT |
creates an HTML report from QTL linkage or association analysis results |
QSASSOCIATION |
performs marker-trait association analysis in a genetically diverse population using bi-allelic and multi-allelic markers |
QSBACKSELECT |
performs a backward selection for loci in single-environment trials |
QSELECTIONINDEX |
calculates (molecular) selection indexes by using phenotypic information and/or molecular scores of multiple traits |
QSESTIMATE |
calculates QTL effects in single-environment trials |
QSIMULATE |
simulates marker data and QTL effects for single and multiple environment trials |
QSQTLSCAN |
performs a genome-wide scan for QTL effects (Simple and Composite Mapping) in single-environment trials |
QTHRESHOLD |
calculates a threshold to identify a significant QTL |
VGESELECT |
selects the best variance-covariance model for a set of environments |