fastme: Tree Estimation Based on the Minimum Evolution Algorithm

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

Description

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

Usage

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  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 vincent.lefort@lirmm.fr

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

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### 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)

Example output



ape documentation built on April 25, 2021, 9:06 a.m.