genSeq

object of class <code>"phylo"</code>.

tree

transition matrix for the simulation. Row and column names (<code>c("a","c","g","t")</code>, although not necessarily in that order) should be provided. If <code>NULL</code>, a single rate is assumed.

multiplier for <code>Q</code>, or a vector for \(\Gamma\) rate heterogeneity.

rate

format of the output object. Can be <code>"DNAbin"</code>, <code>"phyDat"</code>, or <code>"matrix"</code>.

format

Simulates DNA sequence on <code>tree</code> under the specified model. Uses <code>sim.Mk</code> internally.

Simulation

phylogenetics

discrete character

A wide range of functions for phylogenetic analysis - concentrated in phylogenetic comparative biology, but also including numerous methods for visualizing, manipulating, reading or writing, and even inferring phylogenetic trees. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, and simulation of phylogenies and data, for continuous, discrete, and multivariate characters. A broad range of plotting methods for phylogenies and comparative data include, but are not restricted to, methods for mapping trait evolution on trees, for projecting trees into phenotypic space or a geographic map, and for visualizing correlated speciation between trees. Finally, numerous functions are designed for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. For instance, there are functions for randomly or non-randomly attaching species or clades to a phylogeny, for computing consensus phylogenies from a set, for simulating trees and phylogenetic data under a range of models, and for a wide variety of other manipulations and analyses that phylogenetic biologists might find useful in their research.

Liam Revell

phytools

Phylogenetic Tools for Comparative Biology (and Other Things)

genSeq function

<dl>	<dt>tree</dt>
<dd>object of class <code>"phylo"</code>.</dd>	<dt>l</dt>
<dd>length of desired sequences.</dd>	<dt>Q</dt>
<dd>transition matrix for the simulation. Row and column names (<code>c("a","c","g","t")</code>, although not necessarily in that order) should be provided. If <code>NULL</code>, a single rate is assumed.</dd>	<dt>rate</dt>
<dd>multiplier for <code>Q</code>, or a vector for \(\Gamma\) rate heterogeneity.</dd>	<dt>format</dt>
<dd>format of the output object. Can be <code>"DNAbin"</code>, <code>"phyDat"</code>, or <code>"matrix"</code>.</dd>	<dt>...</dt>
<dd>optional arguments.</dd></dl>

Arguments

Liam Revell <a href="/link/liam.revell%40umb.edu?package=phytools&version=1.0-3" data-mini-rdoc="phytools::liam.revell@umb.edu">liam.revell@umb.edu</a>

Author

Simulate a DNA alignment on the tree under a model — genSeq

<dl>

	<dt>tree</dt>
<dd>object of class <code>"phylo"</code>.</dd>

	<dt>l</dt>
<dd>length of desired sequences.</dd>

	<dt>Q</dt>
<dd>transition matrix for the simulation. Row and column names (<code>c("a","c","g","t")</code>, although not necessarily in that order) should be provided. If <code>NULL</code>, a single rate is assumed.</dd>

	<dt>rate</dt>
<dd>multiplier for <code>Q</code>, or a vector for \(\Gamma\) rate heterogeneity.</dd>

	<dt>format</dt>
<dd>format of the output object. Can be <code>"DNAbin"</code>, <code>"phyDat"</code>, or <code>"matrix"</code>.</dd>

	<dt>...</dt>
<dd>optional arguments.</dd>

</dl>

Liam Revell <a href='mailto:liam.revell@umb.edu'>liam.revell@umb.edu</a>

genSeq: Simulate a DNA alignment on the tree under a model

Description

Usage

Value

Arguments

Author

References

Examples