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

genSeq {phytools}

R Documentation

Simulate a DNA alignment on the tree under a model

Simulates DNA sequence on tree under the specified model. Uses sim.history internally.

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

`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.

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

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

## simulate gamma rate heterogeneity
tree<-pbtree(n=26,tip.label=LETTERS)
gg<-rgamma(n=100,shape=0.25,rate=0.25)
X<-genSeq(tree,l=100,rate=gg)

[Package phytools version 0.4-60 Index]