cSPR

<code>cSPR()</code> expects a tree rooted on a single tip.

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

cSPR function

<dl><dt>tree</dt>
<dd>A tree of class <code>phylo</code>.</dd>
<dt>whichMove</dt>
<dd>Integer specifying which SPR move index to perform.</dd></dl>

Arguments

<a href="https://smithlabdurham.github.io/">Martin R. Smith</a>
(<a href="/link/martin.smith%40durham.ac.uk?package=TreeSearch&version=1.5.1" data-mini-rdoc="TreeSearch::martin.smith@durham.ac.uk">martin.smith@durham.ac.uk</a>)

Author

cSPR() expects a tree rooted on a single tip. — cSPR

<dl>

<dt>tree</dt>
<dd>A tree of class <code>phylo</code>.</dd>


<dt>whichMove</dt>
<dd>Integer specifying which SPR move index to perform.</dd>

</dl>

<a href='https://smithlabdurham.github.io/'>Martin R. Smith</a>
(<a href='mailto:martin.smith@durham.ac.uk'>martin.smith@durham.ac.uk</a>)

cSPR: `cSPR()` expects a tree rooted on a single tip.

Description

Usage

Arguments

Author

Examples