Surface of Mars from www.nasa.gov

population genetics

Software OS Webserver Comments
BEAST all No A program for Bayesian MCMC analysis of molecular sequences. Orientated towards molecular clock analyses. Not for constructing phylogenies but rather testing evolutionary hypotheses without preconditioning on a single tree topology. Uses MCMC to average over tree space, so that each tree is weighted proportionally to its posterior probability. Implements a Bayesian generalized skyline plot.
DnaSP Windows No All-time classic! Performs a multitude of tests and analyses, including coalescent simulations. Populations can be mouse-defined.
Arlequin all No Descriptive statistics, neutrality tests, mismatch distribution, AMOVA, Fst, Minimum Spanning Trees, assignment test, (partial) Mantel test, gametic phase estimation; handles sequence, RFLP, and microsatellite data. Latest version (3.x) runs only on Windows.
DMLE+ all No Allows multipoint LD mapping using an arbitrary number of SNPs or microsatellite markers. Implements MCMC methods for Bayesian estimation of the posterior probability density of the position of a disease mutation relative to a set of markers.
HabloBlock all No For haplotype block identification, haplotyping SNPs (or haplotype phasing, resolution or reconstruction) and LD mapping (or genetic association studies). For high-density haplotype or genotype SNP data and is based on a statistical model accounting for recombination hotspots, bottlenecks, genetic drift and mutations and has a Markov Chain in its core.
IM/IMa Windows & *nix Yes/Yes Fits an isolation model with migration to haplotype data drawn from two closely related species or populations. Large numbers of loci can be studied simultaneously, and different mutation models can be used. Uses check-pointing.
MDIV Windows Yes MDIV will simultaneously estimate divergence times and migration rates between two populations under the infinite sites model or under a finite sites model. It assumes a constant population size.
LAMARC all No A package of programs for computing population parameters, such as population size, population growth rate and migration rates by using likelihoods for samples of data (sequences, microsatellites, and electrophoretic polymorphisms) from populations. It approximates the summation of likelihood over all possible gene genealogies that could explain the observed sample.
LARD all No This is a program to detect the presence of recombination in a set of sequences by looking at the set of sequences to discover which are the most plausible parents of a potentially recombinant sequence, and performing a likelihood ratio test for each possible breakpoint position of whether the three-species tree differs on the two sides of the breakpoint.
LDhat all No A program for the analysis of recombination rates from population genetic data.
LIKEWIND *nix No ML-based method for detecting conflicting phylogenetic signal in nucleotide sequence alignments. Detects recombination in divergent sequences.
MANVa All No Multilocus Analysis of Nucleotide Variability. Calculates descriptive statistics and neutrality tests for observed data. Analysis on total/synonymous/nonsynonymous/silent/coding and any other annotated regions given in GFF files. Coalescent simulations are enabled and compared with observed results.
ΜEAdmix Windows No ML estimates of admixture proportions and genetic drift using the coalescent.
Migrate *nix Yes estimates the effective population sizes and migration rates of n constant populations using nonrecombining sequences, microsatellite data or enzyme electrophoretic data. It can run multiple loci in parallel on computer clusters.
MSVAR Windows Yes estimates by MCMC demographic parameters of a single population, such as current and ancestral effective population size and time since Ne change. Flexible priors.
omegaMap *nix Yes Detects natural selection and recombination in DNA or RNA sequences. Residues under selection can be mapped and color-coded using Protein Explorer and MolScript. Distributed with a collection of R scripts.
RDP Windows No Recombination Detection Program applies a number of recombination detection and analysis algorithms. It includes several methods, such as RDP, MaxChi, Chimaera, Geneconv, Bootscan, and Siscan.
RECOMBINE all No This program fits a model which has a single population of constant size with a single recombination rate across all sites. It can accomodate either plain DNA, RNA, or SNP data.
VariScan all No A software package for the analysis of DNA sequence polymorphisms at the whole genome scale. Among other features, the software: (1) can conduct many population genetic analyses; (2) incorporates a multiresolution wavelet transform-based method that allows capturing relevant information from DNA polymorphism data; and (3) it facilitates the visualization of the results in the most commonly used genome browsers.
Comprehensive list of programs for recombination detection.

simulations

Software OS Webserver Comments
ms All No All-time classic engine for coalescent sequence simulations under a Wright-Fisher neutral model.
msHOT All No Modified ms to account for crossover and gene conversion hotspots.
SimCoal2 All No Simulates coalescent events, recombination, migration, demographic fluctuations. DNA, SNPs, microsatellites, RFLP.
SerialSimCoal All No Simulates coalescent events under migration and demographic fluctuations applied to ancient DNA data.
SPLATCHE Windows No Incorporates the influence of the environment in the simulation of migration of a given species from one origin.
AquaSPLATCHE Windows No Simulate genetic diversity based on a realistic vectorized environment.
EvolveAGene All No Simulates coding sequences given a substitution model and selection intensity along a phylogeny. Accomodates indels, too.
Dawg All No Simulates sequences given a GTR substitution model and indel evolution.
Seq-Gen All No Simulates sequences given a substitution model along a phylogeny.
Indel-Seq-Gen *nix No Simulates protein sequences given a substitution model along a phylogeny incorporating info on domains, motifs and indels.
Rose *nix No Simulates sequences given a substitution model along a phylogeny incorporating indels.
mlcoalsim All No Multilocus analyses. Neutrality tests and other statistics, under several demographic models and strong positive selection using the theory of the coalescent. Coalescent simulations accounting for recombination. Simulations conditioned on S and/or Rm values using a rejection algorithm are enabled.
PopG All No One-locus Population genetics simulation program for teaching.

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