rm.gaps

rm.gaps.generic

rm.gaps.multidna

rm.gaps.multiphyDat

rm.gaps,multidna-method

rm.gaps,multiphyDat-method

In multidna and multiphyDat, some individuals may not be sequenced for all genes, resulting in gap-only sequences for missing data.
The generic function <code>rm.gaps</code> has method for both objects; it identifies the missing sequences, and removes gap-only sequences from the alignments wherever needed.

Toolkit for the analysis of multiple gene data (Jombart et al. 2017) <doi:10.1111/1755-0998.12567>.
'apex' implements the new S4 classes 'multidna', 'multiphyDat' and associated methods to handle aligned DNA sequences from multiple genes.

Klaus Schliep

apex

Phylogenetic Methods for Multiple Gene Data

Eric Archer

Rebecca Harris

Thibaut Jombart

Zhian Namir Kamvar

rm.gaps function

<dl><dt>x</dt>
<dd>a multidna or multiphyDat object.</dd>
<dt>...</dt>
<dd>further arguments passed to other methods (currently not used).</dd></dl>

Arguments

Remove gap-only sequences for missing data — rm.gaps

<dl>

<dt>x</dt>
<dd>a multidna or multiphyDat object.</dd>


<dt>...</dt>
<dd>further arguments passed to other methods (currently not used).</dd>

</dl>

Remove gap-only sequences for missing data

rm.gaps: Remove gap-only sequences for missing data

Description

Usage

Arguments