Note: We are pleased that you find programs from the lab to be of interest. Our software gathers many new users each day, and we work hard to include informative error messages and detailed user manuals. We welcome your feedback and wish to facilitate your use of the programs. When questions do arise, it is much appreciated if users put their best effort into making sure that the answer is not in the manual before contacting us. Thanks for your help.
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).
Monophyler [COMING SOON, SPRING 2016]Monophyler computes the probability of monophyly of a specified set of gene lineages conditional on a species tree. Monophyler uses the coalescent together with an arbitrary species tree to determine the monophyly probability for a set of lineages or the reciprocal monophyly probbability for a pair of sets of lineages. It can also accommodate various computations involving three or four lineage sets. The computation is described in "The probability of monophyly of a sample of gene lineages on a species tree" Proceedings of the National Academy of Sciences USA.