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PopGene

Offers a truly large set of methods and statistical tests for the analysis of marker data, including Wright's F-statistics. Nice user interface with simple input format that accommodates codominant and dominant/recessive data types. Unfortunately, does not test F-statistics for statistical significance (see Fstat, GDA, and TFPGA instead). Available for Windows only.

SPAGeDi

SPAGeDi, short for Spatial Pattern Analysis of Genetic Diversity, is a new computer package primarily designed to characterize the spatial genetic structure of mapped individuals and/or mapped populations using codominant or dominant genotype data of any ploidy level. It can compute various statistics describing relatedness or differentiation between individuals or populations by pairwise comparisons, and analyze how these values are related to geographical distances (see also GenAlEx).

Structure Software for Population Genetics Inference

Structure is a software package for using multi-locus genotype data to infer the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including allozymes, microsatellites, RFLPs and SNPs.

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).

ADE-4

ADE-4, short for Ecological Data Analysis 2004, is multifunctional multivariate analysis and graphical display software. Of particular interest here is its spatial data analysis capabilities, which include classical tools for spatial structure analysis, like Ripley's function, as well as a new method to analyze the spatial structure of heterogeneous point patterns. In addition, it works with arbitrarily shaped study regions (see also Programita). Available for the Mac and PC.

Programita

Programita allows you to perform univariate and bivariate point-pattern analysis with Ripley's L-function and the Weigand and MoloneyO-ring statistic. Includes procedures for performing point-pattern analyses for arbitrarily shaped study regions and offers a range of non-standard null models, such as heterogeneous Poisson null models or cluster null models. Documentation is excellent and the associated paper by Weigand and Moloney (2004) is very informative. Available for Windows only.

SADIE Reheated

SADIE, an acronym for Spatial Analysis by Distance IndicEs, is a system developed to do spatial analysis on data from ecology, especially data in the form of counts at spatially-referenced locations. It performs a variety of procedures - see link for details. Available for Windows only. Note: this software is not being updated anymore.

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