Simulates nucleotide data based on parameters under the SELAC model
SelacHMMSimulator(phy, pars, nsites, codon.freq.by.aa = NULL,
codon.freq.by.gene = NULL, numcode = 1, aa.properties = NULL,
nuc.model, include.gamma = FALSE, gamma.type = "quadrature",
ncats = 4, k.levels = 0, diploid = TRUE, site.cats.vector = NULL)The phylogenetic tree with branch lengths.
A vector of parameters used for the simulation. They are ordered as follows: C.q.phi, alpha, beta, Ne, base.freqs for A C G, and the rates for the nucleotide model the very last parameter is always the switching rate of the optimal AA.
Length of the alignment to be simulated
A matrix of codon frequencies for each possible optimal amino acid. Rows are aa (including stop codon), cols are codons.
A matrix of codon frequencies for each gene.
The ncbi genetic code number for translation. By default the standard (numcode=1) genetic code is used.
User-supplied amino acid distance properties. By default we assume Grantham (1974) properties.
Indicates what type nucleotide model to use. There are three options: "JC", "GTR", or "UNREST".
A logical indicating whether or not to include a discrete gamma model.
Indicates what type of gamma distribution to use. Options are "quadrature" after the Laguerre quadrature approach of Felsenstein 2001 or median approach of Yang 1994.
The number of discrete categories.
Provides how many levels in the polynomial. By default we assume a single level (i.e., linear).
A logical indicating whether or not the organism is diploid or not.
A vector designating the rate category for phi when include.gamma=TRUE.
Simulates a nucleotide matrix using parameters under the SELAC model.
Note that the output can be written to a fasta file using the write.dna() function in the ape package.