FastME

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Percentile

Tree Estimation Based on the Minimum Evolution Algorithm

The two FastME functions (balanced and OLS) perform the Minimum Evolution algorithm of Desper and Gascuel (2002).

Keywords
models
Usage
fastme.bal(X, nni = TRUE, spr = TRUE, tbr = TRUE)
  fastme.ols(X, nni = TRUE)
Arguments
X
a distance matrix; may be an object of class "dist".
nni
a boolean value; TRUE to do NNIs (default).
spr
ditto for SPRs.
tbr
ditto for TBRs.
Value

  • an object of class "phylo".

References

Desper, R. and Gascuel, O. (2002) Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle. Journal of Computational Biology, 9(5), 687--705.

See Also

nj, bionj, write.tree, read.tree, dist.dna

Aliases
  • fastme
  • fastme.bal
  • fastme.ols
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 <- fastme.bal(M)
plot(tr, "u")
### a less theoretical example
data(woodmouse)
trw <- fastme.bal(dist.dna(woodmouse))
plot(trw)
Documentation reproduced from package ape, version 2.6-3, License: GPL (>= 2)

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