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.
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.
PASSaGE: Pattern Analysis, Spatial Statistics, and Geographic Exegesis - PASSaGE is a software package designed to aid in the analysis of data in a spatial context. It performs a variety of procedures - see link for details. Available for Windows only.
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.
Salmon Genetics Software | UC Davis Bodega Marine Laboratory - WhichRun is a Windows program that uses multilocus information to assign of individuals to populations and to detect migrant individuals (see also GeneClass and Structure). A web-based version, called DOH, also is available but is slower and the interface isn’t as nice.
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).
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.
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).
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.
PHYLIP - A modular set of programs for phylogenetic analysis. Primarily aimed at the analysis of sequence data, but modules also available for genetic distance estimation, the construction of neighbor-joining and UPGMA trees, and bootstrapping with respect to marker data. Command line interface and peculiar input data format. Available for a variety of operating systems.
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).
Isolation by Distance Web Service - IBDWS, short for Isolation by Distance Web Service, is a web server based application for analyzing the relationship between (genetic) isolation and (geographic) distance. IBDWS works with both diploid genetic marker and haploid DNA sequence data, and for genetic distances calculates Wright's Fst (or PhiST for sequence data), Slatkin's M-hat, and Roussett's linearized Fst. Be sure to the the About IBDWS page for helpful information about using the program: http://ibdws.sdsu.edu/~ibdws/aboutibdws.html
GENEPOP - Web server based software that estimates a variety of population genetic parameters and conducts a variety of sophisticated tests for departures from Hardy-Weinberg, population differentiation, and linkage disequilibrium. It also can convert data files to formats for use with other programs, including Arlequin. Because Genepop runs on the web, it is not operating system specific. If your interest is Wright'sF-statistics, Fstat, GDA, and TFPGA are recommended.
GeneClass 1 & 2 - GeneClass2, short for Genetic Classification, is a program employing multilocus genotypes to select or exclude populations as origins of individuals. Functions include the assignment of individuals to populations and detection of migrants (see also Structure and WhichRun). This command-line program is available for Linux and Windows.
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.
Genetic Data Analysis Software - The primary feature of GDA, short for Genetic Data Analysis, is that it implements the analysis of variance based estimators of Wright's F-statistics advocated by Weir and Cockerham (1984) and Weir (1996) and uses randomization procedures to construct confidence limits about the estimates (see also Fstat and TFPGA). In addition, it calculates basic descriptive statistics, and implements test of linkage disequilibrium. Nice user interface but peculiar input data formatting. Available for Windows.
FSTAT - FSTAT is a computer package for PCs which estimates and tests gene diversities and differentiation statistics from codominant genetic markers. It computes both Nei and Weir & Cockerham families of estimators of gene diversities and F-statistics, and tests them using randomization methods (see also GDA and TFPGA).
CERVUS - CERVUS is a Windows 95-based program designed for large-scale parentage analysis using co-dominant loci. Analysis is broken down into three sequential stages. Using genotype data in text file format, the program can analyse allele frequencies, run appropriate simulations and carry out likelihood-based parentage analysis, testing the confidence of each parentage using the results of the simulation. Simulations may also be used to estimate the power of a series of loci for parentage analysis, using real or imaginary allele frequencies.
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.