bionj: Tree Estimation Based on an Improved Version of the NJ...

In ape: Analyses of Phylogenetics and Evolution

Tree Estimation Based on an Improved Version of the NJ Algorithm

Description

This function performs the BIONJ algorithm of Gascuel (1997).

Usage

bionj(X)

Arguments

X	a distance matrix; may be an object of class "dist".

Value

an object of class "phylo".

Author(s)

original C code by Hoa Sien Cuong and Olivier Gascuel; adapted and ported to R by Vincent Lefort [e-mail]

References

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.

See Also

nj, fastme, mvr, bionjs, SDM, dist.dna

Examples

### 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[lower.tri(M)] <- x
M <- t(M)
M[lower.tri(M)] <- x
dimnames(M) <- list(1:8, 1:8)
tr <- bionj(M)
plot(tr, "u")
### a less theoretical example
data(woodmouse)
trw <- bionj(dist.dna(woodmouse))
plot(trw)

ape documentation built on May 29, 2024, 10:50 a.m.