create_equal_alignment_explicit

function create an alignment with identical information content, using the
explicit method to simulate substitutions

Simulate DNA sequences for the node substitution model.
In the node substitution model, substitutions accumulate additionally
during a speciation event, providing a potential mechanistic explanation for
substitution rate variation. This package provides tools to simulate
such a process, simulate a reference process with only substitutions along
the branches, and provides tools to infer phylogenies from alignments. More
information can be found in Janzen (2021) <doi:10.1093/sysbio/syab085>.

Thijs Janzen

nodeSub

Simulate DNA Alignments Using Node Substitutions

create_equal_alignment_explicit function

<dl><dt>input_tree</dt>
<dd>phylogeny for which to generate alignment</dd>
<dt>sub_rate</dt>
<dd>substitution rate used in the original phylogeny</dd>
<dt>alignment_result</dt>
<dd>result of sim_normal, sim_linked or sim_unlinked</dd>
<dt>verbose</dt>
<dd>provide intermediate output</dd></dl>

Arguments

function create an alignment with identical information content, using the
explicit method to simulate substitutions — create_equal_alignment_explicit

<dl>

<dt>input_tree</dt>
<dd>phylogeny for which to generate alignment</dd>


<dt>sub_rate</dt>
<dd>substitution rate used in the original phylogeny</dd>


<dt>alignment_result</dt>
<dd>result of sim_normal, sim_linked or sim_unlinked</dd>


<dt>verbose</dt>
<dd>provide intermediate output</dd>

</dl>

create_equal_alignment_explicit: function create an alignment with identical information content, using the explicit method to simulate substitutions

Description

Usage

Value

Arguments