https://github.com/cran/ape
Tip revision: b72814286b3390a544fb97d1007fdcc6605b5b7f authored by Emmanuel Paradis on 08 August 2011, 00:00:00 UTC
version 2.7-3
version 2.7-3
Tip revision: b728142
seg.sites.Rd
\name{seg.sites}
\alias{seg.sites}
\title{
Find Segregating Sites in DNA Sequences
}
\usage{
seg.sites(x)
}
\arguments{
\item{x}{a matrix or a list which contains the DNA sequences.}
}
\description{
This function gives the indices of segregating (polymorphic) sites in
a sample of DNA sequences.
}
\details{
If the sequences are in a list, all the sequences must be of the same
length. Ambiguous nucleotides are ignored.
}
\value{
A numeric (integer) vector giving the indices of the segregating
sites.
}
\author{Emmanuel Paradis}
\note{
The present version looks for the sites which are ``variable'' in the
data in terms of different \emph{letters}. This may give unexpected
results if there are ambiguous bases in the data.
}
\seealso{
\code{\link{base.freq}}, \code{\link{GC.content}},
\code{\link{theta.s}}, \code{\link{nuc.div}}
}
\examples{
data(woodmouse)
y <- seg.sites(woodmouse)
y
length(y)
}
\keyword{univar}