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Arlequin 3.5

Offers a large set of methods and statistical tests for population genetic analysis of marker and sequence data, including AMOVA (see also GenAlEx). Nice graphical user interface but peculiar input format for marker data can frustrating (GenAlEx is nicer in this regard). Java based, available for Mac, Windows, and Unix operating systems.

GenAlEx

GenAlEx, short for Genetic Analysis in Excel, is a user-friendly cross-platform package for population genetic analysis. Functions include AMOVA (see also Arlequin), spatial autocorrelation (see also SPAGeDI), Mantel tests (see also Permute! and TFPGA), and principle component analysis of genetic data. It runs within Microsoft Excel and so is not operating system specific. GenAlEx enables population genetic data analysis of codominant, haploid and binary genetic data providing analysis tools applicable to plants and animals.