calc_fraction

calculates the relative contribution of substitutions at
the nodes

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

calc_fraction function

<dl><dt>phy</dt>
<dd>phylogenetic tree (optional)</dd>
<dt>node_time</dt>
<dd>time spent at the node</dd>
<dt>model</dt>
<dd>node substitution model</dd></dl>

Arguments

Calculate the expected fraction of substitutions at the nodes,
relative to the fraction at the branches — calc_fraction

<dl>

<dt>phy</dt>
<dd>phylogenetic tree (optional)</dd>


<dt>node_time</dt>
<dd>time spent at the node</dd>


<dt>model</dt>
<dd>node substitution model</dd>

</dl>

calc_fraction: Calculate the expected fraction of substitutions at the nodes, relative to the fraction at the branches

Description

Usage

Value

Arguments