BIONJ

0th

Percentile

Tree Estimation Based on an Improved Version of the NJ Algorithm

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

Keywords
models
Usage
bionj(X)
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, SDM, dist.dna

Aliases
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)
Documentation reproduced from package ape, version 3.0-2, License: GPL (>= 2)

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