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Descriptive statistics, distances, miscellaneous

Software OS Description
ADZE all Rarefaction for allelic richness, private allelic richness, and private allelic richness for combinations of populations.
Alleles In Space, TFPGA, Mantel-Struct, AMOVA-PREP Windows See website for more info. all Combines allele data of (partly) overlapping size via ML.
CREATE Windows Creates and converts input files for >50 programs.
DISPAN Windows Creates distance trees.
FreeNA Windows Estimates null allele frequencies via a EM algorithm and Fst when null alleles are present via the C2 method.
FSTAT Windows An all-time classic for F-statistics.
GenAlEx all Excel add-in for a variety of analyses (diversity stats, AMOVA, Mantel correlation, PCA, assignment, spatial autocorrelation).
GenClone Windows Analyzes genotypic data, tests for clonality, and describes spatial clonal organization.
GeneDist all Online genetic distance calculator.
GenePop on the web all Webserver implementation of the famous GenePop program.
Genetix Windows A very good program for all kinds of descriptive statistics and FCA. Uses a spreasdsheet entry format and exports in various input formats.
GenoDive MacOS All kinds of analyses, including AMOVA, PCA, k-means clustering, likelihood G-statistic for population differentation, diversity, clone assignment, HWE test, distances, Mantel correlation. Great for data manipulation and input file conversion.
HIERFSTAT R Hierarchical F-statistics in >2 levels using the method of moments. Also tests for population differentation using the likelihood G-statistic.
HP-Rare Windows Rarefaction of private alleles and hierarchical sampling designs.
LinkDos on the web all Webserver for LD estimation.
Microsat all Calculates diversity indices and a variety of distances.
Microsatellite Analyzer (MSA) all Calculates descriptive statistics, distances, F-statistics, and PCR error rates. all Converts the output of Hudson's ms program into microsatellite data. The output could be directly analyzed by MSA.
microsatellite analysis software list URL compiled by David McDonald
Multilocus Package *nix A Mathematica package for the analysis of deterministic multilocus population genetic models.
OptiBin Windows Objective binning of alleles.
POPTREE all Distance trees, heterozygosity measures, Gst.
Populations Windows Distance trees.
PowerMarker Windows Summary statistics, distances, LD, plotting, SNP simulation.
PCAGEN Windows Principal Components Analysis of microsatellite data.
RSTCALC Windows Analyses of population structure, genetic differentiation and gene flow.
standArich R Standardizes sample size before comparing allelic richness estimates. Plots allele distribution/frequency across populations/locus, and the relationship between allelic richness and genet/individual number in a population.
tandem All Automates the binning of microsatellite alleles using a power function.

Population assignment, gene flow, landscape genetics, hybrid zones

Software OS Description
Analyse MacOS For the analysis of geographic variation and hybrid zones.
BAPS all Bayesian assignment of individuals to populations, admixture, and spatial genetics. DNA sequences also accepted as input. Fast!
BELS Windows Selects the most informative combination of loci.
BIMr All Bayesian method that makes inferences about recent proportions of immigrant genes in subdivided populations and that identifies the environmental factors that are responsible for observed gene flow patterns.
COLONISE Windows Determines the composition of the newly colonised population and makes inferences about the factors that influenced individuals to establish a new population. Uses a hierarchical Bayesian model to combine multilocus genotype data with demographic and environmental data, and rjMCMC to get posterior densities.
distruct all Produces nice graphical displays of STRUCTURE results.
CLUMPP all Deals with label switching and multimodality problems in STRUCTURE results.
Doh all Online assignment calculator.
FASTRUCT Windows ML implementation of the classical STRUCTURE model without admixture and uncorrelated allele frequencies relying on expectation-maximization.
GenAlEx all Excel add-in for a variety of analyses (diversity stats, AMOVA, Mantel correlation, PCA, assignment).
GenBMap Windows Infers spatial genetic structure by analyzing genotypes and geographic coordinates simultaneously through a 2D graphical representation.
GeneClass2 Windows Assignment of individuals to populations via ML. Good for ghost populations.
Geneland R Bayesian assignment of individuals to populations using GPS coordinates; estimates the spatial organization on populations.
GESTE Windows A Bayesian method to evaluate the effect that biotic and abiotic environmental factors (geographic distance, language, temperature, altitude, local population sizes, etc.) have on the genetic structure of populations. Good for population processes, such as range expansions, by simply introducing longitude and latitude as the explanatory variables. Estimates Fst values for each local population and relates them to environmental factors using a GLM.
LEA Windows & Linux Likelihood-based estimation of admixture and time since admixture.
LEADMIX Windows ML estimates of admixture proportions and genetic drift.
MLNE Windows ML estimates of Ne and migration rate from the observed temporal and spatial differences in marker allele frequencies.
MixedFamilies all Detects the presence of subfamilies in batches of offspring. Written in Mathematica and R.
NewHybrids Windows & OS9 Uses a Gibbs sampler to estimate the posterior probability that genetically sampled individuals fall into each of a set of user-defined hybrid categories.
Partition Windows Identifies population sub-division (barriers to gene flow) and assigns individuals to populations using a Bayesian method.
PartitionML Windows Searches for the best possible partition of a sample into independent panmictic clusters and simultaneously assign individuals to populations of origin using a ML criterion.
PSMIX R ML inference of population stratification based on expectation-maximization.
SPAGeDi Windows Designed to characterize the spatial genetic structure of mapped individuals and/or mapped populations using genotype data of any ploidy level.
structurama all Bayesian assignment of individuals to populations allowing for the number of populations to vary following a Dirichlet prior.
STRUCTURE all Bayesian assignment of individuals to clusters.
TESS Windows & Linux Bayesian clustering based on a hierarchical mixture model where cluster priors are defined as HMRF. Takes into account geographical coordinates. Compared to BAPS and STRUCTURE on its website.
WombSoft R Analyzes individually georeferenced multilocus genotypes for the inference of genetic boundaries among populations.

Relatedness, parentage

Software OS Description
CERVUS Windows Parentage analysis using allele frequencies and simulations in a ML framework.
COLONY Windows Implements a ML method that assigns individuals in a sample into full-sib families nested within half-sib families (colonies).
FaMoz all Uses likelihood calculation and simulations to perform paternity and parentage studies with codominant, dominant, cytoplasmic markers or combinations of different marker types.
KinInfor Windows Calculates the informativeness of markers in inferring pairwise relatedness or relationships.
MER Windows Moment Estimate of Relatedness.
PARENTE Windows Looks for maternity, paternity, or simultaneously for both potential parents, using multilocus genotypes and birth and death dates of individuals (if available). Also calculates the probability of successfully allocating an individual offspring to its parents.


Software OS Description
DetSel Windows Detects markers responding to selection.
NeutrAllelix Windows Tests microsatellite data for neutrality.
fdist2 Windows Detects loci that might be under selection in samples from structured populations.
Lositan all A selection detection webserver workbench based on the fdist Fst outlier methods.

Population size [changes], Ne estimation

Software OS Description
Bottleneck Windows Implements the method of Cornuet & Luikart (1996 Genetics) for detection of reduction in Ne using allele frequency data.
Geneloss Windows Simulates the effects of bottlenecks on genetic diversity.
GIMLET Windows Estimates population census size using various rarefaction methods. Outputs R scripts for plotting.
JMSv1 Windows Performs a simulation-based evaluation of the diagnostic status of juxtaposed microsatellite systems.
kgtests all Excel add-in to detect signatures of population expansion.
LDNE Windows Ne estimation from linkage disequilibrium data.
M-ratio OSX Estimates M, the ratio of the number of alleles to range in allele size, for a sample of microsatellite loci can be used to detect reductions in Ne.
MCLEEPS OSX Monte Carlo evaluation of the likelihood for Ne from temporally spaced samples.
MISAT Windows Estimates the likelihood surface of the population size parameter q.
msvar/dlik Windows Ne estimation (by the temporal method, too), population size changes.
Nb_HetEx Windows Estimates the effective number of breeders.
ONeSAMP all Webserver for Ne estimation using approximate Bayesian computation.

Genome scanning and detection

Software OS Description
CID all Webserver for the identification and extraction of SSRs from genomic libraries and primer design.
MISA all MIcroSAtellite identification tool.
msatcommander all Locates microsatellite repeats (SSR, VNTR, etc).
Perfect Microsat Repeat Finder www Webserver for STR detection and primer design.
Phobos All Genome scans for microsats, minisats, and sats.
TROLL All A lightweight SSR finder based on a slightly modified Aho-Corasick algorithm.

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