Software
CLUMPP
is a program that deals with label switching and multimodality
problems in population-genetic cluster analyses.
CLUMPP
permutes the clusters output by independent runs of clustering
programs such as
structure,
so that they match up as closely as possible. The user has the option
of choosing one of three algorithms for aligning replicates, with a
tradeoff of speed and similarity to the optimal alignment.
distruct is a program that can be used to graphically display
results produced by the clustering program
structure
or by other similar programs. The figures produced by
distruct display individual membership coefficients in the
same form as used in
"Genetic structure
of human populations" Science 298: 2381-2385
(2002). Various options enable the user to control left-to-right
printing order of populations, bottom-to-top printing order of
clusers, colors, and other graphical details. A program note
describing
distruct was published in
Molecular Ecology Notes 4:
137-138 (2004).
haploconfig is a program that can be used to implement tests
of neutrality based on the frequency distribution of haplotypes in a
sample of DNA sequences (the "haplotype configuration") and the number
of segregating sites. The neutrality tests can be performed
conditional on the standard neutral coalescent model with or without
recombination, exponential population growth, or island migration. A
description of the method underlying the program can be found in
"Statistical tests of the coalescent model
based on the haplotype frequency distribution and the number of
segregating sites" Genetics
169: 1763-1777 (2005). The
haploconfig program can also
be used as a coalescent simulator for models with or without
recombination.
infocalc is a small script for calculating statistics that
measure the ancestry information content of genetic markers. A
description of these statistics can be found in
"Informativeness of genetic markers for
inference of ancestry" American Journal of Human Genetics 73:
1402-1422 (2003), with extensions in
"Algorithms for selecting informative marker panels for population
assignment" Journal of Computational Biology 12: 1183-1201
(2005).
