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)
Arguments
X
a distance matrix; may be an object of class "dist".
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, write.tree, read.tree, dist.dna

Aliases
  • bionj
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[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)
Documentation reproduced from package ape, version 2.7-3, License: GPL (>= 2)

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