statgenlmu/coala: A Framework for Coalescent Simulation

Coalescent simulators can rapidly simulate biological sequences evolving according to a given model of evolution. You can use this package to specify such models, to conduct the simulations and to calculate additional statistics from the results (Staab, Metzler, 2016 <doi:10.1093/bioinformatics/btw098>). It relies on existing simulators for doing the simulation, and currently supports the programs 'ms', 'msms' and 'scrm'. It also supports finite-sites mutation models by combining the simulators with the program 'seq-gen'. Coala provides functions for calculating certain summary statistics, which can also be applied to actual biological data. One possibility to import data is through the 'PopGenome' package (<https://github.com/pievos101/PopGenome>).

Getting started

Package details

AuthorPaul Staab [aut], Dirk Metzler [aut, ths, cre], Jorge E. Amaya Romero [ctb]
MaintainerDirk Metzler <metzler@bio.lmu.de>
LicenseMIT + file LICENSE
Version0.7.2
URL https://github.com/statgenlmu/coala
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("remotes")
remotes::install_github("statgenlmu/coala")
statgenlmu/coala documentation built on March 5, 2024, 10:49 p.m.