\name{FastME}
+\alias{FastME}
\alias{fastme}
\alias{fastme.bal}
\alias{fastme.ols}
Minimum Evolution algorithm of Desper and Gascuel (2002).
}
\usage{
- fastme.bal(X, nni = TRUE)
+ fastme.bal(X, nni = TRUE, spr = TRUE, tbr = TRUE)
fastme.ols(X, nni = TRUE)
}
\arguments{
\item{X}{a distance matrix; may be an object of class \code{"dist"}.}
\item{nni}{a boolean value; TRUE to do NNIs (default).}
+ \item{spr}{ditto for SPRs.}
+ \item{tbr}{ditto for TBRs.}
}
\value{
an object of class \code{"phylo"}.
\seealso{
\code{\link{nj}}, \code{\link{bionj}},
\code{\link{write.tree}}, \code{\link{read.tree}},
- \code{\link{dist.dna}}, \code{\link{mlphylo}}
+ \code{\link{dist.dna}}
}
\examples{
-\dontrun{
### From Saitou and Nei (1987, Table 1):
x <- c(7, 8, 11, 13, 16, 13, 17, 5, 8, 10, 13,
10, 14, 5, 7, 10, 7, 11, 8, 11, 8, 12,
5, 6, 10, 9, 13, 8)
M <- matrix(0, 8, 8)
-M[row(M) > col(M)] <- x
-M[row(M) < col(M)] <- x
-rownames(M) <- colnames(M) <- 1:8
+M[lower.tri(M)] <- x
+M <- t(M)
+M[lower.tri(M)] <- x
+dimnames(M) <- list(1:8, 1:8)
tr <- fastme.bal(M)
plot(tr, "u")
### a less theoretical example
trw <- fastme.bal(dist.dna(woodmouse))
plot(trw)
}
-}
\keyword{models}