Backward-in-time simulation software tools | Population genetics data analysis
Coalescent simulation is pivotal for understanding population evolutionary models and demographic histories, as well as for developing novel analytical methods for genetic association studies for DNA sequence data. A plethora of coalescent simulators are developed, but selecting the most appropriate program remains challenging.
Provides three single-sample estimators and standard temporal method. NeEstimator is suitable for empirical and simulated datasets containing varying numbers of nuclear genotypes consisting of two or more loci and having two or more alleles per locus. It is able to account for missing data calculating a unique fixed-inverse variance-weighted harmonic mean. The tool provides confidence intervals for all methods and in several cases implements new and improved routines.
Computes exact tests or their unbiased estimation for Hardy-Weinberg equilibrium, population differentiation, and two-locus genotypic disequilibrium. Genepop performs analyses of isolation by distance from pairwise comparisons of individuals or population samples, including confidence intervals for neighbourhood size. It allows comparison of differentiation over a given range of geographical distances, in intra vs. inter-ecotypic analyses thank to the implementation of a bootstrap analysis of mean differentiation.
Deduces the barcode gap from the data and to partition the data set using statistical methods. ABGD can be used to obtain the finest partition of a data set into candidate species. It was designed to automates the formulation of species hypotheses. This tool does not infer ancestral states. It can be applied to nuclear sequences that have experienced recombination.
Allows estimation of population-genetic parameters. LAMARC is a genealogy-sampler software that can calculate the population sizes, population exponential growth rates, migration rates, and per-site recombination rate of n populations using DNA, single nucleotide polymorphism (SNP), microsatellite, or electrophoretic data. The software can also perform fine-scale linkage disequilibrium mapping, relating phenotypic data to genetic variation.
An efficient simulator that supports both exact and approximate coalescent simulation with positive selection. cosi2 improves on the speed of existing exact simulators, and permits further speedup in approximate mode while retaining support for selection. cosi2 supports a wide range of demographic scenarios, including recombination hot spots, gene conversion, population size changes, population structure and migration. cosi2 implements coalescent machinery efficiently by tracking only a small subset of the Ancestral Recombination Graph, sampling only relevant recombination events, and using augmented skip lists to represent tracked genetic segments.
Allows for simulation of the genomic diversity of samples drawn from a set of populations with arbitrary patterns of migrations and complex demographic histories, including bottlenecks and various modes of demographic expansion. The main additions to the previous version include the possibility of arbitrary and heterogeneous recombination rates between adjacent loci and multiple coalescent events per generation, allowing for the simulation of very large samples and recombining genomic regions, together with the simulation of single nucleotide polymorphism data with frequency ascertainment bias.
A coalescent simulation program for a structured population with selection at a single diploid locus. MSMS includes the functionality of the simulator ms to model population structure and demography, but adds a model for deme- and time-dependent selection using forward simulations. The program can be used, e.g. to study hard and soft selective sweeps in structured populations or the genetic footprint of local adaptation. The implementation is designed to be easily extendable and widely deployable.