An R tutorial on how to use HHMs to find recombination events in GBS data from a biparental cross.
Files are in R markdown format .Rmd
can be rendered with the push of a buttom from RStudio,
of from any R installation by using the following commands
install.packages("rmarkdown")
setwd("~/your local directory/")
rmarkdown::render("1_BiparentalSim.Rmd")
Files 5_Simulations.Rmd and 6_MoreSimulations.Rmd make thousands of simulations and take about 10 min to render.