fastme: Tree Estimation Based on the Minimum Evolution Algorithm
In gjuggler/ape: Analyses of Phylogenetics and Evolution

Description Usage Arguments Value Author(s) References See Also Examples

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

1 2	fastme.bal(X, nni = TRUE, spr = TRUE, tbr = TRUE) fastme.ols(X, nni = TRUE)

`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.

an object of class "phylo".

original C code by Richard Desper; adapted and ported to R by Vincent Lefort vincent.lefort@lirmm.fr

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.

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

### 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)