4 Tree Estimation Based on an Improved Version of the NJ Algorithm
7 This function performs the BIONJ algorithm of Gascuel (1997).
13 \item{X}{a distance matrix; may be an object of class \code{"dist"}.}
16 an object of class \code{"phylo"}.
19 Gascuel, O. (1997) BIONJ: an improved version of the NJ algorithm
20 based on a simple model of sequence data.
21 \emph{Molecular Biology and Evolution}, \bold{14:}, 685--695.
24 original C code by Hoa Sien Cuong and Olivier Gascuel; adapted and
25 ported to \R by Vincent Lefort \email{vincent.lefort@lirmm.fr}
28 \code{\link{nj}}, \code{\link{fastme}}, \code{\link{mvr}},
29 \code{\link{SDM}}, \code{\link{dist.dna}}
32 ### From Saitou and Nei (1987, Table 1):
33 x <- c(7, 8, 11, 13, 16, 13, 17, 5, 8, 10, 13,
34 10, 14, 5, 7, 10, 7, 11, 8, 11, 8, 12,
40 dimnames(M) <- list(1:8, 1:8)
43 ### a less theoretical example
45 trw <- bionj(dist.dna(woodmouse))