SPAGeDi
Developed by Olivier Hardy and Xavier Vekemans
Description
SPAGeDi (Spatial Pattern Analysis of Genetic Diversity) is a computer package primarily designed to characterise the spatial genetic structure of mapped individuals and/or mapped populations using genotype data of any ploidy level.
It can compute various statistics describing relatedness or differentiation between individuals or populations by pairwise comparisons, and analyse how these values are related to geographical distances, 1°) in a way similar to a spatial autocorrelation analysis, 2°) by linear regressions (the slopes of these regressions can be used to obtain indirect estimates of gene dispersal distances parameters such as neighbourhood size). SPAGeDi can also treat data without spatial information, providing global estimates of genetic differentiation and/or matrices of pairwise statistics between individuals or populations. Data from dominant markers such as AFLP or RAPD can also be treated to estimate pairwise kinship or relationship coefficients between individuals (Hardy 2003 ME.pdf).
The statistics computed include Fst, Rst, Nst, Ds (Nei's standard genetic distance), and (delta mu)2 (Goldstein and Pollok 1997) for analyses at the population level and, for analyses at the individual level, pairwise kinship, relatedness and fraternity coefficients (with different estimators for each) as well as Rousset's distance between individuals and a kinship analogue based on allele size. Jackknife over loci gives approximate standard errors. Permutations of locations, individuals or genes provide ad hoc tests of spatial structure, population differentiation or inbreeding, respectively. A new allele size permutation test also allows to check whether microsatellite allele sizes carry a relevant information about genetic structure (Hardy & al. 2003 Genetics.pdf).
In addition, the actual variance of the statistics can be estimated following the method of Ritland (2000), providing a measure necessary for markerbased inference of the heritability or Qst of quantitative traits.
New version (released March 2015). What's new in SPAGeDi ver 1.5?
Compared to the previous version 1.4, there are several major improvements in this version:
1. SPAGeDi 1.5 can estimate the standardized identity disequilibrium between loci, and thereafter the selfing rate of hermaphrodites, using a population sample of adults genotyped at codominant markers. It is based on the approach of David et al. (2007), extended to autopolyploids by Hardy (2015).
2. SPAGeDi 1.5 can in principle accept datasets up to 100 000 loci, although computer RAM can remain a limitation for performing the computations.
What's new in SPAGeDi ver 1.4?

1. SPAGeDi 1.4 can compute a new estimator of pairwise relatedness between individuals using AFLP or RAPD markers when phenotypes (presence or absence of a band) are affected by non genetic factors. To this end, the broadsense heritability (H2) of each marker must first be estimated using replicated individuals. These H2 estimates are provided at the end of the data file and used to compute corrected estimates of pairwise relatedness coefficients. Details about the statistics used can be found in Ley & Hardy (2013) who showed that H2 is an appropriate measure of the reliability of AFLP markers and that H2 can be much lower than one (the value expected for a “perfect” dominant marker) for the majority of AFLP markers.

2. SPAGeDi 1.4 can compute for each population and locus the effective number of alleles (Nielsen et al. 2003), the rarefied allelic richness for which the subsample size can be specified, and the inbreeding coefficient with significance tests.

3. SPAGeDi 1.4 can test differentiation statistics for each pair of populations.
Computer requirement
SPAGeDi runs on Windows using a simple executable (see below). Source code and native installers for Windows, Mac OS X, and Linux created by Reed A. Cartwright <reed@scit.us> are also available at http://scit.us/spagedi/ .
How to run SPAGeDi
SPAGeDi has no nice userfriendly windows; just launch SPAGeDi.exe and you can draganddrop the data file into the window, the rest is written on the screen, but we suggest that you first have a look at the manual.

SPAGeDi15a(build04032015).exe program for Windows (no installation required)

SPAGeDi_1.5_Manual.pdf manual

SPAGeDi_Data.zip data files
Older versions:

SPAGeDi14c(build17072013).exe program for Windows (no installation required)

SPAGeDi_14_Manual.pdf manual

SPAGeDi_Data.zip data files

SPAGeDi1.3d.exe program for Windows (no installation required)

SPAGeDi1.3awin32.exe for Windows

SPAGeDi1.3aMac.dmg for Mac OS X

SPAGeDi1.3aLinux.tar.gz package to compile for Linux (Linux Binary Package, 2.6 kernel)

SPAGeDi1.3aFrBSD.tar.gz package to compile for Unix (FreeBSD Binary Package, 7.1 kernel)
How to cite SPAGeDi
Hardy OJ, Vekemans X (2002) SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Molecular Ecology Notes 2: 618620.