coalSpeciesTree

<code>coalSpeciesTree</code> estimates species trees and can handle multiple
individuals per species.

cluster

Allows for estimation of phylogenetic trees and networks
using Maximum Likelihood, Maximum Parsimony, distance methods and
Hadamard conjugation (Schliep 2011). Offers methods for tree comparison,
model selection and visualization of phylogenetic networks as described in
Schliep et al. (2017).

Klaus Schliep

phangorn

Phylogenetic Reconstruction and Analysis

Emmanuel Paradis

Leonardo de Oliveira Martins

Alastair Potts

Iris Bardel-Kahr

Tim W. White

Cyrill Stachniss

Michelle Kendall

Keren Halabi

Richel Bilderbeek

Kristin Winchell

Liam Revell

Mike Gilchrist

Jeremy Beaulieu

Brian O'Meara

Long Qu

Joseph Brown

Santiago Claramunt

coalSpeciesTree function

<dl><dt>tree</dt>
<dd>an object of class <code>multiPhylo</code></dd>
<dt>X</dt>
<dd>A <code>phyDat</code> object to define which individual belongs to which
species.</dd>
<dt>sTree</dt>
<dd>A species tree which fixes the topology.</dd></dl>

Arguments

Klaus Schliep <a href="/link/klaus.schliep%40gmail.com?package=phangorn&version=2.11.1" data-mini-rdoc="phangorn::klaus.schliep@gmail.com">klaus.schliep@gmail.com</a> Emmanuel Paradies

Author

Species Tree — coalSpeciesTree

<dl>

<dt>tree</dt>
<dd>an object of class <code>multiPhylo</code></dd>


<dt>X</dt>
<dd>A <code>phyDat</code> object to define which individual belongs to which
species.</dd>


<dt>sTree</dt>
<dd>A species tree which fixes the topology.</dd>

</dl>

Klaus Schliep <a href='mailto:klaus.schliep@gmail.com'>klaus.schliep@gmail.com</a> Emmanuel Paradies

Species Tree

coalSpeciesTree: Species Tree

Description

Usage

Value

Arguments

Author

Details

References

See Also