ape (version 3.0-7)

BIONJ: 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

Value

an object of class "phylo".

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

Run this code
### 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)

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