Arlequin 3.0 is an integrated software package for population genetics data analysis, developed by Laurent Excoffier, Guillaume Laval, and Stefan Schneider. It offers a wide range of methods for analyzing genetic diversity, including the computation of standard genetic diversity indices, estimation of allele and haplotype frequencies, tests of linkage equilibrium, selective neutrality, and demographic equilibrium. New features in Arlequin 3 include a new graphical interface written in C++, robust semantic analysis of input files, and two new methods: Bayesian estimation of gametic phase from multi-locus genotypes and estimation of parameters for instantaneous spatial expansion from DNA sequence polymorphism. The software can handle various data types such as DNA sequences, microsatellite data, and multi-locus genotypes. It also integrates with simulation programs SIMCOAL2 and SPLATCHE to describe genetic diversity under complex evolutionary scenarios. A Windows version of Arlequin 3 is freely available for download, along with a user manual and example files.Arlequin 3.0 is an integrated software package for population genetics data analysis, developed by Laurent Excoffier, Guillaume Laval, and Stefan Schneider. It offers a wide range of methods for analyzing genetic diversity, including the computation of standard genetic diversity indices, estimation of allele and haplotype frequencies, tests of linkage equilibrium, selective neutrality, and demographic equilibrium. New features in Arlequin 3 include a new graphical interface written in C++, robust semantic analysis of input files, and two new methods: Bayesian estimation of gametic phase from multi-locus genotypes and estimation of parameters for instantaneous spatial expansion from DNA sequence polymorphism. The software can handle various data types such as DNA sequences, microsatellite data, and multi-locus genotypes. It also integrates with simulation programs SIMCOAL2 and SPLATCHE to describe genetic diversity under complex evolutionary scenarios. A Windows version of Arlequin 3 is freely available for download, along with a user manual and example files.