reroot {phytools}

Re-root a tree along an edge

Description

Re-roots a phylogenetic tree at an arbitrary position along an edge.

Usage

reroot(tree, node.number, position=NULL, interactive=FALSE, ...)

Arguments

tree

a phylogenetic tree in "phylo" format.

node.number

number of the node descending from the target branch in tree$edge - this can also be a tip in which case the node number is the index number of the tip in tree$tip.label.

position

position along the target edge at which to re-root the tree. If not supplied, then the tree will be re-rooted at the node or tip.

interactive

logical value indicating whether to use interactive mode (defaults to interactive= FALSE).

...

arguments to be passed to plotTree for interactive=TRUE only.

Details

This function had an error for rootings along edges descended from the root node for phytools<=0.2-47. This should be fixed in the present version. Now uses paste.tree, root, and splitTree internally. Earlier versions also had an error related to node labels. This should be fixed in phytools>=0.4-47.

Value

A phylogenetic tree in "phylo" format.

Author(s)

Liam Revell [e-mail]

References

Paradis, E., J. Claude, and K. Strimmer (2004) APE: Analyses of phylogenetics and evolution in R language. Bioinformatics, 20, 289-290.

Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.

See Also

splitTree, paste.tree, root