# fastme: Tree Estimation Based on the Minimum Evolution Algorithm In ape: Analyses of Phylogenetics and Evolution

## Description

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

## Usage

 ```1 2``` ``` 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.

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

## Examples

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15``` ```### 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 5, 2018, 1:03 a.m.