hyphy-class


Class "hyphy"
This class stores information of HYPHY 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

hyphy-class function

 <dl>
<dt><code>fields</code></dt><dd>available features</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>subs</code></dt><dd>sequence substitutions</dd> <dt><code>AA_subs</code></dt><dd>Amino acid sequence substitution</dd> <dt><code>ancseq</code></dt><dd>ancestral sequences</dd> <dt><code>tip_seq</code></dt><dd>tip sequences</dd> <dt><code>tip.fasfile</code></dt><dd>fasta file of tip sequences</dd> <dt><code>tree.file</code></dt><dd>tree file</dd> <dt><code>ancseq.file</code></dt><dd>ancestral sequence file, nexus format</dd> <dt><code>extraInfo</code></dt><dd>extra information</dd> </dl>

hyphy-class: Class "hyphy" This class stores information of HYPHY output

Description

Arguments

Slots

See Also