NucSimulator: Simulate DNA under General-Time Reversible model

In bomeara/selac: Selection Models for Amino Acid and/or Codon Evolution

Description

Simulates nucleotide data based on parameters under the GTR+G model

Usage

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)

Arguments

phy	The phylogenetic tree with branch lengths.
pars	A vector of parameters used for the simulation. They are ordered as follows: gamma shape and the rates for the nucleotide model.
nsites	The number of sites to simulate.
nuc.model	Indicates what type nucleotide model to use. There are three options: "JC", "GTR", or "UNREST".
base.freqs	The base frequencies for A C G T (in that order).
include.gamma	Boolean on whether to use a gamma model
gamma.type	How the gamma bins are used
ncats	The number of discrete gamma categories.
start.vals_array	A vector of nucleotides to be used as the starting nucleotide for each site in the simulation.
user.rate.cats	The user supplied gamma categories to use instead of choosing at random.
user.rates	The user supplied rates to use instead of choosing categories at random.

Details

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.

bomeara/selac documentation built on Nov. 11, 2021, 12:37 a.m.