TreeTools

TreeTools-package

"TreeTools" is an R package that provides functions for creating, modifying and
analysing phylogenetic trees.
It complements packages such as
<a href="https://cran.r-project.org/package=ape">ape</a>,
<a href="https://cran.r-project.org/package=phangorn">phangorn</a> and
<a href="https://cran.r-project.org/package=phytools">phytools</a>,
aiming for efficient and robust implementations of functions, typically
applied to unweighted trees (i.e. those without edge lengths).

internal

Efficient implementations of functions for the creation,
modification and analysis of phylogenetic trees.
Applications include:
generation of trees with specified shapes;
tree rearrangement;
analysis of tree shape;
rooting of trees and extraction of subtrees;
calculation and depiction of split support;
plotting the position of rogue taxa (Klopfstein & Spasojevic 2019)
<doi:10.1371/journal.pone.0212942>;
calculation of ancestor-descendant relationships,
of 'stemwardness' (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>,
and of tree balance (Mir et al. 2013, Lemant et al. 2022)
<doi:10.1016/j.mbs.2012.10.005>, <doi:10.1093/sysbio/syac027>;
artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>;
import and export of trees from Newick, Nexus (Maddison et al. 1997)
<doi:10.1093/sysbio/46.4.590>,
and TNT <https://www.lillo.org.ar/phylogeny/tnt/> formats;
and analysis of splits and cladistic information.

Martin R. Smith

Create, Modify and Analyse Phylogenetic Trees

Emmanuel Paradis

Robert Noble

TreeTools-package function

Maintainer: Martin R. Smith <a href="/link/martin.smith%40durham.ac.uk?package=TreeTools&version=1.12.0" data-mini-rdoc="TreeTools::martin.smith@durham.ac.uk">martin.smith@durham.ac.uk</a> (<a href="https://orcid.org/0000-0001-5660-1727">ORCID</a>) [copyright holder]
Other contributors:<ul>
<li>Emmanuel Paradis (<a href="https://orcid.org/0000-0003-3092-2199">ORCID</a>) [copyright holder]</li>
<li>Robert Noble (<a href="https://orcid.org/0000-0002-8057-4252">ORCID</a>) [copyright holder]</li>
</ul>

Author

"TreeTools" is an R package that provides functions for creating, modifying and
analysing phylogenetic trees.
It complements packages such as
<a href='https://cran.r-project.org/package=ape'>ape</a>,
<a href='https://cran.r-project.org/package=phangorn'>phangorn</a> and
<a href='https://cran.r-project.org/package=phytools'>phytools</a>,
aiming for efficient and robust implementations of functions, typically
applied to unweighted trees (i.e. those without edge lengths).

TreeTools — TreeTools-package

Maintainer: Martin R. Smith <a href='mailto:martin.smith@durham.ac.uk'>martin.smith@durham.ac.uk</a> (<a href='https://orcid.org/0000-0001-5660-1727'>ORCID</a>) [copyright holder]
Other contributors:<ul>
<li>Emmanuel Paradis (<a href='https://orcid.org/0000-0003-3092-2199'>ORCID</a>) [copyright holder]</li>
<li>Robert Noble (<a href='https://orcid.org/0000-0002-8057-4252'>ORCID</a>) [copyright holder]</li>
</ul>

TreeTools-package: TreeTools

Description

Arguments

Author

Details

See Also