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 randomisation methods.
Jackknife and Bootstrap confidence intervals are also provided. The windows
version also estimates statistics developed for the stepwise mutation model
(Rst and the like).
HIERFSTAT
hierfstat is a package for R allowing to estimate F-statistics and variance
components with the methods of moments for any number of levels in a
hierarchy. The package also allows to test the significance of population
differentiation using the likelihood ratio G-statistic or the variance
components.
quantiNEMO
quantiNEMO is an individual-based, genetically explicit stochastic simulation
program. It was developed to investigate the effects of selection, mutation,
recombination, and drift on quantitative traits with varying architectures in
structured populations connected by migration and located in a
heterogeneous habitat. quantiNEMO is highly flexible at various levels:
population, selection, trait(s) architecture, genetic map for QTL and/or
markers, environment, demography, mating system, etc.
PCAGEN
PCAGEN is a computer package for Windows which performs Principal
Component Analysis (PCA) on gene frequency data. Graphical ordinations of
samples are provided and graphs can be saved. Using randomizations, the
program also tests the significance of total inertia as well as individual axes
inertia.

BIASDISP
BIASDISP is now included in FSTAT.

A software developed by Jrme Goudet.

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 Fstatistics, and tests them using randomisation methods. The current version
(Feb. 2002) is 2.9.3.2. Previous versions are not maintained anymore. However,
if you still run DOS, you can still download the old version (1.2) below.
To install FSTAT 2.9.3, double click the file fstat293dist.exe once you have
downloaded it. This will create under the folder you have chosen the following
architecture of folders and files:
Fstat293.exe
Fstat293.hlp
Fstat293.cnt
Readme.txt
Readme.doc
In order to read the help file, you will need to install winhlp32.exe
The following folders contain data and example files, use of which is detailed in the
help file:
.\data
.\data\bias dispersal
.\data\multiple regression
What FSTAT does
From a data set of codominant or haploid genetic markers, FSTAT calculates the
following:
- Number of individuals per sample and loci.
- Allele frequency estimated per sample and overall.
- Observed and expected number of each genotype per sample and locus.
- Unbiased gene diversity per sample and locus.
- Number of alleles sampled per locus and sample, as well as overall.
- [NEW] Allelic richness per locus and sample, as well as overall samples
- Fis per locus and sample, as well as a test of whether it is significantly positive or
negative (significant deficit and excess of heterozygotes respectively).

- Nei's (1987) estimators of gene diversities and differentiation.

- Weir & Cockerham (1984) Capf (Fit), theta (Fst) and smallf (Fis) estimated per
allele, per locus and overall. FSTAT also calculates Hamilton's (1971) relatedness
relat=2Fst/(1+Fit), calculated using an estimator strictly equivalent to Queller and
Goodnight's (1989). This measure is the average relatedness of individuals within
samples when compared to the whole data set.
Confidence intervals based on resampling schemes are provided for Weir &
Cockerham statistics:
- Jackknifing per locus over samples is performed. The resampling unit are the
different samples. This procedure is only carried out if there are more than 4
samples.
- Jackknifing over loci. In this case, the resampling units are the different loci. This
procedure is only carried out if there are more than 4 loci.
- Bootstrapping over loci. Bootstrapping over loci is performed only when there is
more than 4 loci in the data set.
- Estimation of R- statistics (Slatkin, 1995), specifically designed for microsatellite
undergoing stepwise mutations.
- Estimation of Fst (theta) per pair of samples.
- Overall test whether each sample at each locus is in HW equilibrium.
- Test whether the entire data set is in HW equilibrium.
- Test whether samples are differentiated assuming either that there is HW within
samples or that there is not (Only one of these 2 tests can be carried out).
- Test whether each sample at each locus is in Hardy-Weinberg (HW) equilibrium.
- Test whether each pair of samples is differentiated. The tests do not assume
random mating within samples. A table of significant pairwise differentiation after
corrections for multiple testing is produced.
- [NEW] Test whether each pair of loci in each sample and overall is at genotypic
equilibrium
- [NEW] Test whether groups of samples differ for a large panel of statistics
- [NEW] Test whether categories of individuals differ in dispersal rates (four
different tests)
- [NEW] Convert FSTAT format to GENEPOP and vice- versa
- [NEW] Performs multiple regression or Partial Mantel tests