fastme: Tree Estimation Based on the Minimum Evolution Algorithm

Description Usage Arguments 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 = 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".

Author(s)

original C code by Richard Desper; adapted and ported to R by Vincent Lefort [email protected]

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

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)

ape documentation built on May 30, 2017, 6:11 a.m.