# dist.topo

##### Topological Distances Between Two Trees

This function computes the topological distance between two
phylogenetic trees or among trees in a list (if `y = NULL`

using
different methods.

- Keywords
- manip

##### Usage

`dist.topo(x, y = NULL, method = "PH85")`

##### Arguments

- x
an object of class

`"phylo"`

or of class`"multiPhylo"`

.- y
an (optional) object of class

`"phylo"`

.- method
a character string giving the method to be used: either

`"PH85"`

, or`"score"`

.

##### Details

Two methods are available: the one by Penny and Hendy (1985, originally from Robinson and Foulds 1981), and the branch length score by Kuhner and Felsenstein (1994). The trees are always considered as unrooted.

The topological distance is defined as twice the number of internal branches defining different bipartitions of the tips (Robinson and Foulds 1981; Penny and Hendy 1985). Rzhetsky and Nei (1992) proposed a modification of the original formula to take multifurcations into account.

The branch length score may be seen as similar to the previous distance but taking branch lengths into account. Kuhner and Felsenstein (1994) proposed to calculate the square root of the sum of the squared differences of the (internal) branch lengths defining similar bipartitions (or splits) in both trees.

##### Value

a single numeric value if both `x`

and `y`

are used, an
object of class `"dist"`

otherwise.

##### Note

The geodesic distance of Billera et al. (2001) has been disabled: see the package distory on CRAN.

##### References

Billera, L. J., Holmes, S. P. and Vogtmann, K. (2001) Geometry of the
space of phylogenetic trees. *Advances in Applied Mathematics*,
**27**, 733--767.

Kuhner, M. K. and Felsenstein, J. (1994) Simulation comparison of
phylogeny algorithms under equal and unequal evolutionary rates.
*Molecular Biology and Evolution*, **11**, 459--468.

Nei, M. and Kumar, S. (2000) *Molecular Evolution and
Phylogenetics*. Oxford: Oxford University Press.

Penny, D. and Hendy, M. D. (1985) The use of tree comparison
metrics. *Systemetic Zoology*, **34**, 75--82.

Robinson, D. F. and Foulds, L. R. (1981) Comparison of phylogenetic
trees. *Mathematical Biosciences*, **53**, 131--147.

Rzhetsky, A. and Nei, M. (1992) A simple method for estimating and
testing minimum-evolution trees. *Molecular Biology and
Evolution*, **9**, 945--967.

##### See Also

##### Examples

```
# NOT RUN {
ta <- rtree(30)
tb <- rtree(30)
dist.topo(ta, ta) # 0
dist.topo(ta, tb) # unlikely to be 0
# }
```

*Documentation reproduced from package ape, version 5.3, License: GPL (>= 2)*