R: Roots Phylogenetic Trees

root {ape} | R Documentation

## Roots Phylogenetic Trees

### Description

`root` reroots a phylogenetic tree with respect to the specified outgroup or at the node specified in `node`.

`unroot` unroots a phylogenetic tree, or returns it unchanged if it is already unrooted.

`is.rooted` tests whether a tree is rooted.

### Usage

    root(phy, ...)
    ## S3 method for class 'phylo'
    root(phy, outgroup, node = NULL, resolve.root = FALSE,
         interactive = FALSE, edgelabel = FALSE, ...)
    ## S3 method for class 'multiPhylo'
    root(phy, outgroup, ...)

    unroot(phy)
    ## S3 method for class 'phylo'
    unroot(phy)
    ## S3 method for class 'multiPhylo'
    unroot(phy)

    is.rooted(phy)
    ## S3 method for class 'phylo'
    is.rooted(phy)
    ## S3 method for class 'multiPhylo'
    is.rooted(phy)

### Arguments

`phy` | an object of class `"phylo"` or `"multiPhylo"`.
`outgroup` | a vector of mode numeric or character specifying the new outgroup.
`node` | alternatively, a node number where to root the tree.
`resolve.root` | a logical specifying whether to resolve the new root as a bifurcating node.
`interactive` | if `TRUE` the user is asked to select the node by clicking on the tree which must be plotted.
`edgelabel` | a logical value specifying whether to treat node labels as edge labels and thus eventually switching them so that they are associated with the correct edges when using `drawSupportOnEdges` (see Czech et al. 2016).
`...` | arguments passed among methods (e.g., when rooting lists of trees).

### Details

The argument `outgroup` can be either character or numeric. In the first case, it gives the labels of the tips of the new outgroup; in the second case the numbers of these labels in the vector `phy$tip.label` are given.

If `outgroup` is of length one (i.e., a single value), then the tree is rerooted using the node below this tip as the new root.

If `outgroup` is of length two or more, the most recent common ancestor (MRCA) of the ingroup is used as the new root. Note that the tree is unrooted before being rerooted, so that if `outgroup` is already the outgroup, then the returned tree is not the same than the original one (see examples). If `outgroup` is not monophyletic, the operation fails and an error message is issued.

If `resolve.root = TRUE`, `root` adds a zero-length branch below the MRCA of the ingroup.

A tree is considered rooted if either only two branches connect to the root, or if there is a `root.edge` element. In all other cases, `is.rooted` returns `FALSE`.

### Value

an object of class `"phylo"` or `"multiPhylo"` for `root` and `unroot`; a logical vector for `is.rooted`.

### Note

The use of `resolve.root = TRUE` together with `node =` gives an error if the specified node is the current root of the tree. This is because there is an ambiguity when resolving a node in an unrooted tree with no explicit outgroup. If the node is not the current root, the ambiguity is solved arbitrarily by considering the clade on the right of `node` (when the tree is plotted by default) as the ingroup. See a detailed explanation there:

http://www.mail-archive.com/r-sig-phylo@r-project.org/msg03805.html.

### Author(s)

Emmanuel Paradis

### References

Czech, L., Huerta-Cepas, J. and Stamatakis, A. (2016) A critical review on the use of support values in tree viewers and bioinformatics toolkits. http://dx.doi.org/10.1101/035360

### See Also

`bind.tree`, `drop.tip`, `nodelabels`, `identify.phylo`

### Examples

    data(bird.orders)
    plot(root(bird.orders, 1))
    plot(root(bird.orders, 1:5))

    tr <- root(bird.orders, 1)
    is.rooted(bird.orders) # yes
    is.rooted(tr)          # no
    ### This is because the tree has been unrooted first before rerooting.
    ### You can delete the outgroup...
    is.rooted(drop.tip(tr, "Struthioniformes"))
    ### ... or resolve the basal trichotomy in two ways:
    is.rooted(multi2di(tr))
    is.rooted(root(bird.orders, 1, r = TRUE))
    ### To keep the basal trichotomy but forcing the tree as rooted:
    tr$root.edge <- 0
    is.rooted(tr)

    x <- setNames(rmtree(10, 10), LETTERS[1:10])
    is.rooted(x)

[Package ape version 5.1 Index]