sim_normal_explicit

simulate a sequence assuming substitutions are only accumulated along the
branches, using the explicit simulation method (e.g. reverse substitutions
are modeled explicitly)

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

sim_normal_explicit function

<dl><dt>x</dt>
<dd>a phylogenetic tree <code>tree</code>, i.e. an object of class
<code>phylo</code> or and object of class <code>pml</code>.</dd>
<dt>l</dt>
<dd>length of the sequence to simulate.</dd>
<dt>Q</dt>
<dd>the rate matrix.</dd>
<dt>bf</dt>
<dd>base frequencies.</dd>
<dt>rootseq</dt>
<dd>a vector of length l containing the root sequence, other root
sequence is randomly generated.</dd>
<dt>rate</dt>
<dd>mutation rate or scaler for the edge length, a numerical value
greater than zero.</dd></dl>

Arguments

simulate a sequence assuming substitutions are only accumulated along the
branches, using the explicit simulation method (e.g. reverse substitutions
are modeled explicitly) — sim_normal_explicit

<dl>

<dt>x</dt>
<dd>a phylogenetic tree <code>tree</code>, i.e. an object of class
<code>phylo</code> or and object of class <code>pml</code>.</dd>


<dt>l</dt>
<dd>length of the sequence to simulate.</dd>


<dt>Q</dt>
<dd>the rate matrix.</dd>


<dt>bf</dt>
<dd>base frequencies.</dd>


<dt>rootseq</dt>
<dd>a vector of length l containing the root sequence, other root
sequence is randomly generated.</dd>


<dt>rate</dt>
<dd>mutation rate or scaler for the edge length, a numerical value
greater than zero.</dd>

</dl>

simulate a sequence assuming substitutions are only accumulated along the
branches, using the explicit simulation method (e.g. reverse substitutions
are modeled explicitly)

sim_normal_explicit: simulate a sequence assuming substitutions are only accumulated along the branches, using the explicit simulation method (e.g. reverse substitutions are modeled explicitly)

Description

Usage

Value

Arguments