reroot

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

utilities

phylogenetics

A wide range of methods for phylogenetic analysis - concentrated in phylogenetic comparative biology, but also including numerous techniques for visualizing, analyzing, manipulating, reading or writing, and even inferring phylogenetic trees. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, and simulation of phylogenies and trait data. A broad range of plotting methods for phylogenies and comparative data include (but are not restricted to) methods for mapping trait evolution on trees, for projecting trees into phenotype space or a onto a geographic map, and for visualizing correlated speciation between trees. Lastly, numerous functions are designed for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. For instance, there are functions for computing consensus phylogenies from a set, for simulating phylogenetic trees and data under a range of models, for randomly or non-randomly attaching species or clades to a tree, as well as for a wide range of other manipulations and analyses that phylogenetic biologists might find useful in their research.

Liam Revell

phytools

Phylogenetic Tools for Comparative Biology (and Other Things)

reroot function

<dl>	<dt>tree</dt>
<dd>a phylogenetic tree in <code>"phylo"</code> format.</dd>	<dt>node.number</dt>
<dd>number of the node descending from the target branch in <code>tree$edge</code> - this can also be a tip in which case the node number is the index number of the tip in <code>tree$tip.label</code>.</dd>	<dt>position</dt>
<dd>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.</dd>	<dt>interactive</dt>
<dd>logical value indicating whether to use interactive mode (defaults to <code>interactive=</code> <code>FALSE</code>).</dd>	<dt>...</dt>
<dd>arguments to be passed to <code>plotTree</code> for <code>interactive=TRUE</code> only.</dd></dl>

Arguments

Liam Revell <a href="/link/liam.revell%40umb.edu?package=phytools&version=2.1-1" data-mini-rdoc="phytools::liam.revell@umb.edu">liam.revell@umb.edu</a>

Author

Re-root a tree along an edge — reroot

<dl>

	<dt>tree</dt>
<dd>a phylogenetic tree in <code>"phylo"</code> format.</dd>

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

	<dt>position</dt>
<dd>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.</dd>

	<dt>interactive</dt>
<dd>logical value indicating whether to use interactive mode (defaults to <code>interactive=</code> <code>FALSE</code>).</dd>

	<dt>...</dt>
<dd>arguments to be passed to <code>plotTree</code> for <code>interactive=TRUE</code> only.</dd>

</dl>

Liam Revell <a href='mailto:liam.revell@umb.edu'>liam.revell@umb.edu</a>

reroot: Re-root a tree along an edge

Description

Usage

Value

Arguments

Author

Details

References

See Also