# FastME

From ape v3.2
by Emmanuel Paradis

##### Tree Estimation Based on the Minimum Evolution Algorithm

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

- Keywords
- models

##### 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"`

.

##### 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

##### 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)
```

*Documentation reproduced from package ape, version 3.2, License: GPL (>= 2)*

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