<code>CI</code> and <code>RI</code> compute the Consistency Index (CI) and Retention
Index (RI).

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

CI function

<dl><dt>tree</dt>
<dd>tree to start the nni search from.</dd>
<dt>data</dt>
<dd>A object of class phyDat containing sequences.</dd>
<dt>cost</dt>
<dd>A cost matrix for the transitions between two states.</dd>
<dt>sitewise</dt>
<dd>return CI/RI for alignment or sitewise</dd></dl>

Arguments

Consistency Index and Retention Index — CI

<dl>

<dt>tree</dt>
<dd>tree to start the nni search from.</dd>


<dt>data</dt>
<dd>A object of class phyDat containing sequences.</dd>


<dt>cost</dt>
<dd>A cost matrix for the transitions between two states.</dd>


<dt>sitewise</dt>
<dd>return CI/RI for alignment or sitewise</dd>

</dl>

Consistency Index and Retention Index

CI: Consistency Index and Retention Index

Description

Usage

Arguments

Details

See Also