Given a set of marker, phenotypic trait, and (where applicable)
map data, QGene does the following. Highlighted
items are new features of QGene 3.0
for the Power PC.
- Displays all three types of data in interactive graphical
form.
- Performs fast simple and multiple regression analysis of
traits using markers and marker interactions, and regression-based
interval analysis for placing QTLs on a genetic map. Single-marker
analysis is also performed on categorical traits.
Displays contours for up to 20 trait
analyses at once and exports them in a "stacked" plot.
- Performs fast permutation tests
in simple interval mapping.
- Permits comparison among all individuals in a population
or variety panel with respect to their marker genotypes
and their
phenotypes, identifying individuals
by user-assigned names.
- Allows rapid visual gauging of correlation between any two
phenotypic traits and produces a correlation matrix for all traits.
- Allows viewing of molecular-marker genotypes in which chromosomal
regions derived from either parent can be distinguished by pattern
or color.
Exports
selected sets of chromosome genotype plots.
- Shows and evaluates segregation for all markers and shows genotype segment distribution at locus,
individual, and population levels.
- Produces statistics on genome ratio, crossover frequency,
and segment length by chromosome, locus, and/or genotype.
- Generates simulated maps and populations based on them, according
to user's specifications for population type, chromosome and
marker numbers, QTL numbers, gene action, etc. These populations
can be advanced by any of several breeding schemes and their
marker and trait data can be saved.
- Allows construction of an elementary selection index on marker
alleles and assesses the probability of generating near-isogenic
lines for selected genomic regions.
- Provides estimated 2-point marker linkages,
including for dominant markers in
heterozygous populations.
- Performs analyses on any of 12 line-cross population types:
both standard mapping populations and others developed by various
combinations of selfing and backcrossing. Version
3.0 includes some analyses of a cross between outbreeders.
- Permits exploration of multiple-trait field-trial data and creates interactive Finlay-Wilkinson stability
plots.
- Produces multiple-trait maps for rapid visual association
of trait associations by chromosome.
- Evaluates multilocus probes for their ability to discriminate
genotypes.
- Permits simultaneous truncation selection on any combination
of traits.
- Permits analysis of subsets of a population following selection
on phenotype or genotype.
- And does a few other things.
