1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
|
\name{genSeq}
\alias{genSeq}
\title{Simulate a DNA alignment on the tree under a model}
\usage{
genSeq(tree, l=1000, Q=NULL, rate=1, format="DNAbin", ...)
}
\arguments{
\item{tree}{object of class \code{"phylo"}.}
\item{l}{length of desired sequences.}
\item{Q}{transition matrix for the simulation. Row and column names \code{c("a","c","g","t")} (although not necessarily in that order, should be provided. If \code{NULL}, a single rate is assumed.}
\item{rate}{multiplier for \code{Q}, or a vector for Gamma rate heterogeneity.}
\item{format}{format of the output object. Can be \code{"DNAbin"}, \code{"phyDat"}, or \code{"matrix"}.}
\item{...}{optional arguments.}
}
\description{
Simulates DNA sequence on \code{tree} under the specified model. Uses \code{\link{sim.history}} internally.
}
\value{
An object of class \code{"DNAbin"} or \code{"phyDat"}, or a matrix of nucleotides.
}
\references{
Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). \emph{Methods Ecol. Evol.}, \bold{3}, 217-223.
}
\author{Liam Revell \email{liam.revell@umb.edu}}
\examples{
## 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)
}
\keyword{phylogenetics}
\keyword{simulation}
|
