keep_tips

keep_tips.phylo

keep_tips.multiPhylo

keep_tips.rankedPhylo

Prune a tree or a collection of trees and keep only requested tips.

Calculate RNNI distance between and manipulate with ranked trees. RNNI stands for Ranked Nearest Neighbour Interchange and is an extension of the classical NNI space (space of trees created by the NNI moves) to ranked trees, where internal nodes are ordered according to their heights (usually assumed to be times). The RNNI distance takes the tree topology into account, as standard NNI does, but also penalizes changes in the order of internal nodes, i.e. changes in the order of times of evolutionary events. For more information about the RNNI space see: Gavryushkin et al. (2018) <doi:10.1007/s00285-017-1167-9>, Collienne & Gavryushkin (2021) <doi:10.1007/s00285-021-01567-5>, Collienne et al. (2021) <doi:10.1007/s00285-021-01685-0>, and Collienne (2021) <http://hdl.handle.net/10523/12606>.

Jiří Moravec

rrnni

Manipulate with RNNI Tree Space

Lena Collienne

keep_tips function

<dl><dt>x</dt>
<dd>a tree of class "phylo" or "multiPhylo"</dd>
<dt>tips</dt>
<dd>tip labels to keep</dd></dl>

Arguments

Prune a tree — keep_tips

<dl>

<dt>x</dt>
<dd>a tree of class "phylo" or "multiPhylo"</dd>


<dt>tips</dt>
<dd>tip labels to keep</dd>

</dl>

keep_tips: Prune a tree

Description

Usage

Value

Arguments

Examples