7 Tree Estimation Based on the Minimum Evolution Algorithm
10 The two FastME functions (balanced and OLS) perform the
11 Minimum Evolution algorithm of Desper and Gascuel (2002).
14 fastme.bal(X, nni = TRUE, spr = TRUE, tbr = TRUE)
15 fastme.ols(X, nni = TRUE)
18 \item{X}{a distance matrix; may be an object of class \code{"dist"}.}
19 \item{nni}{a boolean value; TRUE to do NNIs (default).}
20 \item{spr}{ditto for SPRs.}
21 \item{tbr}{ditto for TBRs.}
24 an object of class \code{"phylo"}.
27 Desper, R. and Gascuel, O. (2002) Fast and accurate phylogeny
28 reconstruction algorithms based on the minimum-evolution principle.
29 \emph{Journal of Computational Biology}, \bold{9(5)}, 687--705.
32 original C code by Richard Desper; adapted and ported to R
33 by Vincent Lefort \email{vincent.lefort@lirmm.fr}
36 \code{\link{nj}}, \code{\link{bionj}},
37 \code{\link{write.tree}}, \code{\link{read.tree}},
38 \code{\link{dist.dna}}
41 ### From Saitou and Nei (1987, Table 1):
42 x <- c(7, 8, 11, 13, 16, 13, 17, 5, 8, 10, 13,
43 10, 14, 5, 7, 10, 7, 11, 8, 11, 8, 12,
49 dimnames(M) <- list(1:8, 1:8)
52 ### a less theoretical example
54 trw <- fastme.bal(dist.dna(woodmouse))