SelonSimulator: Simulate DNA under the SELON model
In selac: Selection Models for Amino Acid and/or Codon Evolution

Simulates nucleotide data based on parameters under the SELAC model

1 2	SelonSimulator(phy, pars, nuc.optim_array, nuc.model, diploid = TRUE, start.vals_array = NULL)

`phy`	The phylogenetic tree with branch lengths.
`pars`	A vector of parameters used for the simulation. They are ordered as follows: a0, a1, a2, Ne, base.freqs for A C G, and the nucleotide rates.
`nuc.optim_array`	A vector of optimal nucleotide for each site to be simulated.
`nuc.model`	Indicates what type nucleotide model to use. There are three options: "JC", "GTR", or "UNREST".
`diploid`	A logical indicating whether or not the organism is diploid or not.
`start.vals_array`	A vector of nucleotides to be used as the starting nucleotide for each site in the simulation.

Simulates a nucleotide matrix using parameters under the SELON model. Note that the output can be written to a fasta file using the write.dna() function in the ape package.

selac documentation built on July 1, 2020, 10:08 p.m.