This function computes the Swofford--Olsen--Waddell--Hillis (SOWH) test, a parametric bootstrap test. The function is computational very demanding and likely to be very slow.

## Usage

```
SOWH.test(x, n = 100, restricted = list(optNni = FALSE), optNni = TRUE,
trace = 1, ...)
```

## Arguments

- x
an object of class

`"pml"`

.- n
the number of bootstrap replicates.

- restricted
list of restricted parameter settings.

- optNni
Logical value indicating whether topology gets optimized (NNI).

- trace
Show output during computations.

- ...
Further arguments passed to

`"optim.pml"`

.

## Value

an object of class SOWH. That is a list with three elements, one is a matrix containing for each bootstrap replicate the (log-) likelihood of the restricted and unrestricted estimate and two pml objects of the restricted and unrestricted model.

## Details

`SOWH.test`

performs a parametric bootstrap test to compare two trees.
It makes extensive use `simSeq`

and `optim.pml`

and can take quite
long.

## References

Goldman, N., Anderson, J. P., and Rodrigo, A. G. (2000)
Likelihood -based tests of topologies in phylogenetics. *Systematic
Biology* **49** 652-670.

Swofford, D.L., Olsen, G.J., Waddell, P.J. and Hillis, D.M. (1996)
Phylogenetic Inference in Hillis, D.M., Moritz, C. and Mable, B.K. (Eds.)
*Molecular Systematics* (2nd ed.) 407-514, Sunderland, MA: Sinauer

## Author

Klaus Schliep klaus.schliep@gmail.com

## Examples

```
# in real analysis use larger n, e.g. 500 preferably more
if (FALSE) {
data(Laurasiatherian)
dm <- dist.logDet(Laurasiatherian)
tree <- NJ(dm)
fit <- pml(tree, Laurasiatherian)
fit <- optim.pml(fit, TRUE)
set.seed(6)
tree <- rNNI(fit$tree, 1)
fit <- update(fit, tree = tree)
(res <- SOWH.test(fit, n=100))
summary(res)
}
```