Suboptimality

internal

Reconstruct phylogenetic trees from discrete data.
Inapplicable character states are handled using the algorithm of Brazeau,
Guillerme and Smith (2019) <doi:10.1093/sysbio/syy083> with the "Morphy"
library, under equal or implied step weights.
Contains a "shiny" user interface for interactive tree search and exploration
of results, including character visualization, rogue taxon detection,
tree space mapping, and cluster consensus trees (Smith 2022a, b)
<doi:10.1093/sysbio/syab099>, <doi:10.1093/sysbio/syab100>.
Profile Parsimony (Faith and Trueman, 2001) <doi:10.1080/10635150118627>,
Successive Approximations (Farris, 1969) <doi:10.2307/2412182>
and custom optimality criteria are implemented.

Martin R. Smith

TreeSearch

Phylogenetic Analysis with Discrete Character Data

Martin Brazeau

Suboptimality function

<dl><dt>trees</dt>
<dd>list of trees, to include an optimal tree</dd>
<dt>proportional</dt>
<dd>logical stating whether to normalise results to lowest
score</dd></dl>

Arguments

Tree suboptimality — Suboptimality

<dl>

<dt>trees</dt>
<dd>list of trees, to include an optimal tree</dd>


<dt>proportional</dt>
<dd>logical stating whether to normalise results to lowest
score</dd>

</dl>

Suboptimality: Tree suboptimality

Description

Usage

Value

Arguments