New Features in Version 4.1

This is a brief summary of the differences between versions 4.0 and 4.1.  For
linguistic clarity, option 12 is now named "Cases and Controls" rather than
"Genetic Homogeneity."  The keyword PEDIGREES_IN_SECOND_POPULATION has been
replaced by the keyword POPULATION_FACTOR.  This substitution allows testing for
differences in allele frequencies among more than two populations in option 6
and greater flexibility in designating permutation units for case and control
individuals in option 12.  Mendel's ability to read LINKAGE pedigree files has
been enhanced.  There is no longer a need for a trait locus. When it exists, it
may be any locus in the locus file.  The keyword AFFECTED_LOCUS_OR_FACTOR is
used to identify which locus is the trait locus.  A second model has been added
to option 11 that permits testing for linkage equilibrium between all pairs of
loci, not just between adjacent pairs.  Under this model, Mendel reports an
adjusted chi-squared statistic and Lewontin's D' measure of linkage
disequilibrium.  Finally, option 12 now accommodates association testing with
matched case/control designs.  Computation of p-values is done via permutation
units, which are exchangeable groups of people such as sibships, spouse pairs,
or a random sample from the same population.  Permutation of case/control labels
is performed only within each permutation unit rather than across the entire
data set.