Code

code for simulation of gene tree within species tree with sampling. requirements: R packages "ape", "apTreeshape" SIMCOAL (SIMCOAL must be in your working directory) codes: simulation.R: an example code for simulations used in the manuscripts gene.tree.simulations.R: functions used to run SIMCOAL simulation, sample species and simulate species trees simcoal.functions.R: functions for running SIMCOAL from R sample.lineage.R: functions for sampling species from trees usage: "gene.tree.simulations.R", "simcoal.functions.R" and "sample.lineage.R" include functions used to run simulations. "simulation.R" is a code to call these functions and run a simulation. put the four R script files and SIMCOAL in a directory. Then set your working directory to it (setwd("...")). run codes in simulation.R by source("./simulation.R") or copy and paste the codes.