paml_rst-class

set.subs,paml_rst-method

set.subs<-,paml_rst-method


Class "paml_rst"
This class stores information of rst file from PAML output


classes

ggtree extends the ggplot2 plotting system which implemented the
grammar of graphics. ggtree is designed for visualizing phylogenetic tree
and different types of associated annotation data.

Guangchuang Yu

ggtree

a phylogenetic tree viewer for different types of tree annotations

paml_rst-class function

 <dl>
<dt><code>fields</code></dt><dd>availabel attributes</dd> <dt><code>treetext</code></dt><dd>tree text</dd> <dt><code>phylo</code></dt><dd>phylo object</dd> <dt><code>seq_type</code></dt><dd>one of "NT" and "AA"</dd> <dt><code>tip_seq</code></dt><dd>sequences of tips</dd> <dt><code>marginal_ancseq</code></dt><dd>Marginal reconstruction of ancestral sequences</dd> <dt><code>joint_ancseq</code></dt><dd>Joint reconstruction of ancestral sequences</dd> <dt><code>marginal_subs</code></dt><dd>sequence substitutions based on marginal_ancseq</dd> <dt><code>joint_subs</code></dt><dd>sequence substitutions based on joint_ancseq</dd> <dt><code>marginal_AA_subs</code></dt><dd>Amino acid sequence substitutions based on marginal_ancseq</dd> <dt><code>joint_AA_subs</code></dt><dd>Amino acid sequence substitutions based on joint_ancseq</dd> <dt><code>rstfile</code></dt><dd>rst file</dd> <dt><code>extraInfo</code></dt><dd>extra information</dd> </dl>

paml_rst-class: Class "paml_rst" This class stores information of rst file from PAML output

Description

Arguments

Slots

See Also