Forward-in-time simulation software tools | Population genetics data analysis
In population genetics, simulation is a fundamental tool for analyzing how basic evolutionary forces such as natural selection, recombination, and mutation shape the genetic landscape of a population. Forward simulation represents the most powerful, but, at the same time, most compute-intensive approach for simulating the genetic material of a population.
Predicts gene diversity over a sampling area. Biotools is an R package that allows users to obtain spatial unbiased estimates of gene diversity from molecular datasets. This program was designed to perform and work with cluster analysis, discriminant analysis and path analysis (standard and under collinearity). It also contains the new tests for genetic covariance components.
A forward-time population genetics simulation environment. The core of simuPOP is a scripting language (Python) that provides a large number of objects and functions to manipulate populations, and a mechanism to evolve populations forward in time. Using this R/Splus-like environment, users can create, manipulate and evolve populations interactively, or write a script and run it as a batch file.
Provides a flexible and powerful tool for simulating molecular sequence evolution. INDELible is a portable and flexible application for generating nucleotide, amino acid and codon sequence data by simulating insertions and deletions (indels) as well as substitutions. Indels are simulated under several models of indel-length distribution. The program implements a rich repertoire of substitution models, including the general unrestricted model and nonstationary nonhomogeneous models of nucleotide substitution, mixture, and partition models that account for heterogeneity among sites, and codon models that allow the nonsynonymous/synonymous substitution rate ratio to vary among sites and branches.
Generates samples from populations with complex demographic histories under various models of natural selection. SFS_CODE performs simulations under a general Wright-Fisher model with arbitrary demographic, selective, and mutational effects. It allows the user to simulate realistic genomic regions with several loci evolving according to a variety of mutation models (from simple to context-dependent), and takes into account insertions and deletions. Each locus can be annotated as either coding or non-coding, sex-linked or autosomal, selected or neutral, and have an arbitrary linkage structure.
A flexible and efficient simulation software and a rescaling technique have been developed to aid computational efficiency that together allow the simulation of sequence-level data over large genomic regions in entire diploid populations under various scenarios for demography, mutation, selection, and recombination, the latter including hotspots and gene conversion.
Estimates the ancestries and leverages them for their association with phenotypes. POPSICLE separates the genome into non-overlapping sliding windows of user defined size. It attributes the local profiles to the existing clades or the new clades as needed. This tool deduces ancestries and determinants of phenotype. It is useful to unravel cross-species genome-wide similarities.
Offers a platform dedicated to population genetics datasets simulations. EASYPOP is a standalone software that can handle haploid, diploid, and haplodiploid organisms according a wide range of mating systems. The program contains various migration such as hierarchical island model as well as mutation models. The application generates outputs directly compatible with a processing through FSTAT, GENEPOP, and ARLEQUIN software.