Coalescent Theory - Software

Software

A large body of software exists for both simulating data sets under the coalescent process as well as inferring parameters such as population size and migration rates from genetic data.

• TreesimJ Forward simulation software allowing sampling of genealogies and data sets under diverse selective and demographic models.
• BEAST - Bayesian MCMC inference package with a wide range of coalescent models including the use of temporally sampled sequences.
• CoaSim - software for simulating genetic data under the coalescent model.
• GeneRecon - software for the fine-scale mapping of linkage disequilibrium mapping of disease genes using coalescent theory based on an 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
• 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.
• Migrate - Maximum likelihood and Bayesian inference of migration rates under the n-coalescent. The inference is implemented using MCMC
• Migraine - A program which implements coalescent algorithms for a maximum likelihood analysis (using Importance Sampling algortihms) of genetic data with a focus on spatially structured populations .
• Lamarc - software for estimation of rates of population growth, migration, and recombination.
• 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.
• SARG - Structure Ancestral Recombination Graph by Magnus Nordborg
• simcoal2 -software to simulate genetic data under the coalescent model with complex demography and recombination
• Recodon and NetRecodon -software to simulate coding sequences with inter/intracodon recombination, migration, growth rate and longitudinal sampling .
• COAL - Program for computing gene tree probabilities and simulating gene trees in species trees under the coalescent model .
• IBDSim - A computer package for the simulation of genotypic data under general isolation by distance models .