GapHandler

Gaps represented by the inapplicable token can be treated as "missing data",
i.e. as equivalent to the ambiguous token <code>?</code>; as an extra state, equivalent
to other states such as <code>0</code> or <code>1</code>; or as "inapplicable data" using the
algorithm of Brazeau, Guillerme and Smith (2019).

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

GapHandler function

<dl><dt>morphyObj</dt>
<dd>Object of class <code>morphy</code>, perhaps created with
<code>PhyDat2Morphy()</code>.</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

Read how a Morphy Object handles the inapplicable token — GapHandler

<dl>

<dt>morphyObj</dt>
<dd>Object of class <code>morphy</code>, perhaps created with
<code>PhyDat2Morphy()</code>.</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>)

GapHandler: Read how a Morphy Object handles the inapplicable token

Description

Usage

Value

Arguments

Author

See Also

Examples