sim_normal

Simulate sequences for a given evolutionary tree, using a standard model
of sequence evolution along the branches. Code for this function was heavily
inspired by the function <code>simSeq</code> from the phangorn package.

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 function

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

Arguments

Klaus Schliep <a href="/link/klaus.schliep%40gmail.com?package=nodeSub&version=1.2.8" data-mini-rdoc="nodeSub::klaus.schliep@gmail.com">klaus.schliep@gmail.com</a>

Author

Simulate sequences for a given evolutionary tree, using a standard model
of sequence evolution along the branches. Code for this function was heavily
inspired by the function simSeq from the phangorn package. — sim_normal

<dl>

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

</dl>

Klaus Schliep <a href='mailto:klaus.schliep@gmail.com'>klaus.schliep@gmail.com</a>

Simulate sequences for a given evolutionary tree, using a standard model
of sequence evolution along the branches. Code for this function was heavily
inspired by the function <code>simSeq</code> from the phangorn package.

sim_normal: Simulate sequences for a given evolutionary tree, using a standard model of sequence evolution along the branches. Code for this function was heavily inspired by the function `simSeq` from the phangorn package.

Description

Usage

Value

Arguments

Author