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Description:BayesAss is a program that estimates recent migration rates between populations using MCMC. It also estimates each individual's immigrant ancestry, the generation in which immigration occurred (i.e. the individual can be assigned as an immigrant from a specific population, a non-immigrant, or the offspring of an immigrant and a non-immigrant), the population (as opposed to the sample) allele frequencies, inbreeding (F) values within each population, and genotypes at any locus with missing data. Details of the method can be found in: Wilson GA, and B Rannala. 2003. Bayesian inference of recent migration rates using multilocus genotypes. Genetics 163(3): 1177-1191. BayesAss requires diploid data, and can be used for genetic systems such as microsatellites, RFLPs, SNPs, and allozymes. The method assumes relatively low levels of migration, and the proportion of migrant individuals into a population cannot exceed 1/3 of the population total each generation. Loci are assumed to be in linkage equilibrium, but deviations from Hardy-Weinberg equilibrium are allowable. The method does not check for the presence of null alleles, and their occurrence may negatively affect the results. Estimates are most accurate when a large number of variable loci are used, sample size is large, and population differentiation is high, as described in the paper mentioned above. The program is available in Windows and C++ versions.
Input Parameters:
 - Input
 - Seed
 - Iterations
 - Sampling Frequency
 - Burnin
 - Delta Value for Allele Frequency
 - Delta Value for Migration Rate
 - Delta Value for Inbreeding (F) Value
 - Print User-Defined Settings
 - Print Genotype and Sampling Information
 - Print Mean and variance of the posterior probabilities for each allele
 - Print Mean and variance of the posterior probabilities for each inbreeding (F) value
 - Print Individual Assignments
 - Print Posterior probabilities for missing data
 - Print Summary of assignments over populations
 - Print Mean and variance of the posterior probabilities for each migration rate
 - Print Number of Changes
 - Print The number of times each frequency falls within 0.05 intervals
 - Print Changes in log likelihood values
 - Print Distribution of log likelihood values
Output Parameters:
 - Output
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