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}},
29 \code{\link{write.tree}}, \code{\link{read.tree}},
30 \code{\link{dist.dna}}, \code{\link{mlphylo}}
33 ### From Saitou and Nei (1987, Table 1):
34 x <- c(7, 8, 11, 13, 16, 13, 17, 5, 8, 10, 13,
35 10, 14, 5, 7, 10, 7, 11, 8, 11, 8, 12,
38 M[row(M) > col(M)] <- x
39 M[row(M) < col(M)] <- x
40 rownames(M) <- colnames(M) <- 1:8
43 ### a less theoretical example
45 trw <- bionj(dist.dna(woodmouse))