simurg: Simulate a Bacterial Pangenome in R

This R package is intended to produce simulated pangenomes using reference sequences as starting point (MRCA), and both Neutral and Infinitely Many Genes (IMG) models to produce changes along branches of a simulated coalescent tree.

Installation

The simplest way of installing simurg is using devtools package:

if (!require(devtools)) {
    install.packages('devtools')
    library(devtools)
}
 
install_github('iferres/simurg')

Help

The main function of simurg is well documented. Once the package is loaded, please refer to:

help('simpg')

Vignettes

A vignette is also provided to learn more about this package. If you want to see it locally, you have to build it first when installing simurg:

library(devtools)
install_github('iferres/simurg', build_vignettes = TRUE)
vignette('Simulate_a_bacterial_pangenome')

Also, visit the Wiki page to see the vignette example.