genSeq: Simulate a DNA alignment on the tree under a model

In phytools: Phylogenetic Tools for Comparative Biology (and Other Things)

Simulate a DNA alignment on the tree under a model

Description

Simulates DNA sequence on tree under the specified model.

Usage

genSeq(tree, l=1000, Q=NULL, rate=1, format="DNAbin", ...)

Arguments

tree	object of class "phylo".
l	length of desired sequences.
Q	transition matrix for the simulation. Row and column names (c("a","c","g","t"), although not necessarily in that order) should be provided. If NULL, a single rate is assumed.
rate	multiplier for Q, or a vector for \Gamma rate heterogeneity.
format	format of the output object. Can be "DNAbin", "phyDat", or "matrix".
...	optional arguments.

Details

Uses sim.Mk internally.

Value

An object of class "DNAbin" or "phyDat", or a matrix of nucleotides.

Author(s)

Liam Revell [e-mail]

References

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.

Examples

data(mammal.tree)
mammal.tree$edge.length<-mammal.tree$edge.length/
    max(nodeHeights(mammal.tree))*0.2 ## rescale tree
## simulate gamma rate heterogeneity
gg<-rgamma(n=100,shape=0.25,rate=0.25)
dna<-genSeq(mammal.tree,l=100,rate=gg)

phytools documentation built on Nov. 10, 2023, 1:08 a.m.