genSeq {phytools}

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. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.

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)