BIONJ {ape} | R Documentation |
This function performs the BIONJ algorithm of Gascuel (1997).
bionj(X)
X |
a distance matrix; may be an object of class "dist" . |
an object of class "phylo"
.
original C code by Hoa Sien Cuong and Olivier Gascuel; adapted and ported to R by Vincent Lefort vincent.lefort@lirmm.fr
Gascuel, O. (1997) BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Molecular Biology and Evolution, 14:, 685–695.
nj
, fastme
,
write.tree
, read.tree
,
dist.dna
, mlphylo
### 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 tr <- bionj(M) plot(tr, "u") ### a less theoretical example data(woodmouse) trw <- bionj(dist.dna(woodmouse)) plot(trw)