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Bioinformatics 24: 2498-2504 (2008).
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. A program note describing CLUMPP was published in Bioinformatics 23: 1801-1806 (2007).
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).
"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.
"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).
"A maximum likelihood method to correct for allelic dropout in microsatellite data with no replicate genotypes" Genetics 192: 651-669 (2012).
"The probability of monophyly of a sample of gene lineages on a species tree" Proceedings of the National Academy of Sciences USA 113: 8002-8009 (2016), Monophyler calculates the probability of monophyly for a set of lineages or the reciprocal monophyly probability for a pair of sets of lineages. (2) Using "The probability of reciprocal monophyly of gene lineages in three and four species" Theoretical Population Biology 129: 133-147 (2019), it calculates various monophyly probabilities involving three or four lineage sets in three-taxon and four-taxon species trees. (3) Finally, using "The probability of joint monophyly of samples of gene lineages for all species in an arbitrary species tree", it calculates the probability of reciprocal monophyly for an arbitrary number of sets of lineages on an arbitrary species tree.