on a Bayesian MCMC framework. genetree software for estimation of population genetics parameters using coalescent theory and simulation (the R package popgen). See also Oxford Mathematical Genetics and Bioinformatics Group GENOME – rapid coalescent-based whole-genome simulation IBDSim – a computer package for the simulation of genotypic data under general isolation by distance models. IMa – IMa implements the same Isolation with Migration model, but does so using a new method that provides estimates of the joint posterior probability density of the model parameters. IMa also allows log likelihood ratio tests of nested demographic models. IMa is based on a method described in Hey and Nielsen (2007 PNAS 104:2785–2790). IMa is faster and better than IM (i.e. by virtue of providing access to the joint posterior density function), and it can be used for most (but not all) of the situations and options that IM can be used for. Lamarc – software for estimation of rates of population growth, migration, and recombination. Migraine – a program which implements coalescent algorithms for a maximum likelihood analysis (using Importance Sampling algorithms) of genetic data with a focus on spatially structured populations. Migrate – maximum likelihood and Bayesian inference of migration rates under the n-coalescent. The inference is implemented using MCMC MaCS – Markovian Coalescent Simulator – simulates genealogies spatially across chromosomes as a Markovian process. Similar to the SMC algorithm of McVean and Cardin, and supports all demographic scenarios found in Hudson's ms. ms & msHOT – Richard Hudson's original program for generating samples under neutral models and an extension which allows recombination hotspots. msms – an extended version of ms that includes selective sweeps. msprime – a fast and scalable ms-compatible simulator, allowing demographic simulations, producing compact output files for thousands or millions of genomes. Recodon and NetRecodon – software to simulate coding sequences with inter/intracodon recombination, migration, growth rate and longitudinal sampling. CoalEvol and SGWE – software to simulate nucleotide, coding and amino acid sequences under the coalescent with demographics, recombination, population structure with migration and longitudinal sampling. SARG – structure Ancestral Recombination Graph by Magnus Nordborg simcoal2 – software to simulate genetic data under the coalescent model with complex demography and recombination TreesimJ – forward simulation software allowing sampling of genealogies and data sets under diverse selective and demographic models. References Sources Articles Arenas, M. and Posada, D. (2014) Simulation of Genome-Wide Evolution under Heterogeneous Substitution Models and Complex Multispecies