sort.multiPhylo

==.phylo

&lt;.phylo

&gt;.phylo

==.MixedBase

&lt;.MixedBase

&gt;.MixedBase

Trees are sorted by their mixed base representation,
treating their leaves in the order of their labels (i.e. alphabetically,
if leaves are labelled with text).

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

TreeTools

Create, Modify and Analyse Phylogenetic Trees

Emmanuel Paradis

Robert Noble

sort.multiPhylo function

<dl><dt>x, decreasing, na.last, ...</dt>
<dd>As in <code><a href="/link/sort()?package=TreeTools&version=1.12.0" data-mini-rdoc="TreeTools::sort()">sort()</a></code>.</dd>
<dt>e1, e2</dt>
<dd>Objects to be compared.</dd></dl>

Arguments

<a href="https://orcid.org/0000-0001-5660-1727">Martin R. Smith</a>
(<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>)

Author

Sort a list of phylogenetic trees — sort.multiPhylo

<dl>

<dt>x, decreasing, na.last, ...</dt>
<dd>As in <code><a href='https://rdrr.io/r/base/sort.html'>sort()</a></code>.</dd>


<dt>e1, e2</dt>
<dd>Objects to be compared.</dd>

</dl>

<a href='https://orcid.org/0000-0001-5660-1727'>Martin R. Smith</a>
(<a href='mailto:martin.smith@durham.ac.uk'>martin.smith@durham.ac.uk</a>)

sort.multiPhylo: Sort a list of phylogenetic trees

Description

Usage

Arguments

Author

Examples