fastme: Tree Estimation Based on the Minimum Evolution Algorithm

In ape: Analyses of Phylogenetics and Evolution

Tree Estimation Based on the Minimum Evolution Algorithm

Description

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

Usage

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

Arguments

X	a distance matrix; may be an object of class "dist".
nni	a logical value; TRUE to perform NNIs (default).
spr	ditto for SPRs.
tbr	ignored (see details).

Details

The code to perform topology searches based on TBR (tree bisection and reconnection) did not run correctly and has been removed after the release of ape 5.3. A warning is issued if tbr = TRUE.

Value

an object of class "phylo".

Author(s)

original C code by Richard Desper; adapted and ported to R by Vincent Lefort [e-mail]

References

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

See Also

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

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 <- fastme.bal(M)
plot(tr, "u")
### a less theoretical example
data(woodmouse)
trw <- fastme.bal(dist.dna(woodmouse))
plot(trw)

ape documentation built on May 29, 2024, 10:50 a.m.