DoubleNNI

the first column of the edge matrix of a tree of class
<code><a rd-options="" href="/link/phylo?package=TreeSearch&version=0.3.2" data-mini-rdoc="TreeSearch::phylo">phylo</a></code>, i.e. <code>tree$edge[, 1]</code>

parent

the second column of the edge matrix of a tree of class
<code><a rd-options="" href="/link/phylo?package=TreeSearch&version=0.3.2" data-mini-rdoc="TreeSearch::phylo">phylo</a></code>, i.e. <code>tree$edge[, 2]</code>

child

(optional) integer specifying the index of an edge to bisect/prune,
generated randomly if not specified.
Alternatively, set to <code>-1</code> to return a complete list
of all trees one step from the input tree.

edgeToBreak

Returns the edge parameter of the two trees consistent with the speficied <acronym>NNI</acronym> rearrangement

internal

Searches for phylogenetic trees that are optimal using a user-defined criterion.
Implements Profile Parsimony (Faith and Trueman, 2001) <doi:10.1080/10635150118627>, and
Successive Approximations (Farris, 1969) <doi:10.2307/2412182>.
Handles inapplicable data using the algorithm of Brazeau, Guillerme and Smith
(2019) <doi:10.1093/sysbio/syy083>.

Martin R. Smith

TreeSearch

Phylogenetic Tree Search Using Custom Optimality Criteria

Emmanuel Paradis

Klaus Schliep

Martin Brazeau

DoubleNNI function

the first column of the edge matrix of a tree of class
<code><a rd-options='' href='phylo'>phylo</a></code>, i.e. <code>tree$edge[, 1]</code>

the second column of the edge matrix of a tree of class
<code><a rd-options='' href='phylo'>phylo</a></code>, i.e. <code>tree$edge[, 2]</code>

DoubleNNI: Double NNI

Description

Usage

Arguments

Value