Arlequin 3.0 is an integrated software package for population genetics data analysis. It includes methods for computing genetic diversity indices, estimating allele and haplotype frequencies, testing for linkage equilibrium, selective neutrality, and demographic equilibrium, as well as analyzing population subdivision under the AMOVA framework. Arlequin 3 introduces a new C++ graphical interface, improved input file parsing, and two new methods: Bayesian estimation of gametic phase from multi-locus genotypes and estimation of parameters of an instantaneous spatial expansion from DNA sequence polymorphism. The software can handle various data types, including DNA sequences, microsatellite data, and standard multi-locus genotypes. A Windows version is freely available at http://cmpg.unibe.ch/software/arlequin3. Arlequin provides methods for analyzing genetic diversity within and between populations. Intra-population methods include maximum-likelihood estimation of allele and haplotype frequencies, estimation of gametic phase, demographic expansion parameters, and tests of linkage disequilibrium and Hardy-Weinberg equilibrium. Inter-population methods include analysis of population subdivision, computation of genetic distances, exact tests of population differentiation, and assignment tests of individual genotypes to populations. New features in Arlequin 3 include the ELB algorithm for gametic phase estimation, an EM zipper algorithm for haplotype frequency estimation, and a method for estimating parameters of a spatial expansion from DNA sequence polymorphism. The software also includes a more robust input file parsing procedure, compatibility with modern web browsers, and improved confidence interval estimation for F-statistics under the AMOVA framework. Arlequin is available for free download and includes an updated user manual.Arlequin 3.0 is an integrated software package for population genetics data analysis. It includes methods for computing genetic diversity indices, estimating allele and haplotype frequencies, testing for linkage equilibrium, selective neutrality, and demographic equilibrium, as well as analyzing population subdivision under the AMOVA framework. Arlequin 3 introduces a new C++ graphical interface, improved input file parsing, and two new methods: Bayesian estimation of gametic phase from multi-locus genotypes and estimation of parameters of an instantaneous spatial expansion from DNA sequence polymorphism. The software can handle various data types, including DNA sequences, microsatellite data, and standard multi-locus genotypes. A Windows version is freely available at http://cmpg.unibe.ch/software/arlequin3. Arlequin provides methods for analyzing genetic diversity within and between populations. Intra-population methods include maximum-likelihood estimation of allele and haplotype frequencies, estimation of gametic phase, demographic expansion parameters, and tests of linkage disequilibrium and Hardy-Weinberg equilibrium. Inter-population methods include analysis of population subdivision, computation of genetic distances, exact tests of population differentiation, and assignment tests of individual genotypes to populations. New features in Arlequin 3 include the ELB algorithm for gametic phase estimation, an EM zipper algorithm for haplotype frequency estimation, and a method for estimating parameters of a spatial expansion from DNA sequence polymorphism. The software also includes a more robust input file parsing procedure, compatibility with modern web browsers, and improved confidence interval estimation for F-statistics under the AMOVA framework. Arlequin is available for free download and includes an updated user manual.