Simulates nucleotide data based on parameters under the GTR+G model
NucSimulator(phy, pars, nsites, nuc.model, base.freqs,
include.gamma = TRUE, gamma.type = "median", ncats = 4,
start.vals_array = NULL, user.rate.cats = NULL, user.rates = NULL)The phylogenetic tree with branch lengths.
A vector of parameters used for the simulation. They are ordered as follows: gamma shape and the rates for the nucleotide model.
The number of sites to simulate.
Indicates what type nucleotide model to use. There are three options: "JC", "GTR", or "UNREST".
The base frequencies for A C G T (in that order).
Boolean on whether to use a gamma model
How the gamma bins are used
The number of discrete gamma categories.
A vector of nucleotides to be used as the starting nucleotide for each site in the simulation.
The user supplied gamma categories to use instead of choosing at random.
The user supplied rates to use instead of choosing categories at random.
Simulates a nucleotide matrix using parameters under the GTR+G model. Note that the output can be written to a fasta file using the write.dna() function in the ape package.