sim.codon: Simulate a codon sequence alignment

In synDss: Recombination detection using synonymous distances

Description

This function uses PAML to simulate sequences under codon models.

Usage

sim.codon(n.taxa, n.codons, reps, tree, freqs = c(0.6, 0.3, 0.1), omega = c(0.1, 0.8, 3.2), kap = 2, call="evolverNSsites 6")

Arguments

n.taxa	Number of taxa
n.codons	Number of codons
reps	Number of replicate datasets to simulate
tree	Phylogenetic tree, as an object of class "phylo"
freqs	The p parameter
omega	The omega paramater
kap	The kappa parameter
call	The call to the evolver executable, with option "6" by default to indicate a simulation of codon sequences

Value

A list of simulated codon alignments

Author(s)

Peter Chi [e-mail]

References

Z. Yang. PAML 4: phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution, 24:1586-1591, 2007.

synDss documentation built on May 2, 2019, 5:40 p.m.