code.simple.gaps

<code>code.simple.gaps</code> takes an aligned DNA sequence matrix and codes the simple gaps, i.e. gaps that do not overlap with other gaps. The gapped positions are excluded from the matrix and the coded gap characters are appended to the matrix.

Functions that wrap popular phylogenetic software for sequence
alignment, masking of sequence alignments, and estimation of phylogenies and
ancestral character states.

Martin R. Smith

Interfaces to Phylogenetic Software in R

Christoph Heibl

Natalie Cusimano

Franz-Sebastian Krah

code.simple.gaps function

<dl> <dt>x</dt>
<dd>An object of class <code>DNAbin</code>.</dd> 
 <dt>append</dt>
<dd>Logical.</dd></dl>

Arguments

Author

Simple Gap/Indel Coding — code.simple.gaps

<dl>

 <dt>x</dt>
<dd>An object of class <code>DNAbin</code>.</dd>

 
 <dt>append</dt>
<dd>Logical.</dd>

</dl>

code.simple.gaps: Simple Gap/Indel Coding

Description

Usage

Value

Arguments

Author

References

See Also