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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.

Permute!

Not population genetics software per se but very handy for conducting multiple regression over distance with permutation tests (e.g, Mantel test; see also GenAlEx and TFPGA). Unlike other programs can conduct permuation tests using non-square matrices (important in some contexts). Nice user interface with simple input format. Available for the Mac only (a Classic application).

TFPGA genetic data analysis software

TFPGA, short for Tools for Population Genetic Analyses, is a program for the analysis of allozyme and molecular population genetic data that calculates descriptive statistics, genetic distances, F-statistics, and tests for Hardy-Weinberg equilibrium (see also Fstat and GDA). It also performs exact tests for genetic differentiation (see GenePop), Mantel tests (see GenAlEx and Permute!), and UPGMA cluster analyses (see GDA and Phylip).