R: Tree Estimation Based on the Minimum Evolution Algorithm

FastME {ape} | R Documentation

## 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 = 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 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(5), 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)

[Package ape version 5.0 Index]