## microsatellites

**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. |

combi.pl | 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. |

ms2ms.pl | 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. |

**Selection**

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*estimationSoftware | 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. |

Email me if you think a program should be listed here.