hyphy-class {treeio} | R Documentation

## Class "hyphy" This class stores information of HYPHY output

### Description

Class "hyphy" This class stores information of HYPHY output

### Slots

`fields`

  available features

`treetext`

  tree text

`phylo`

  phylo object

`seq_type`

  one of "NT" and "AA"

`subs`

  sequence substitutions

`AA_subs`

  Amino acid sequence substitution

`ancseq`

  ancestral sequences

`tip_seq`

  tip sequences

`tip.fasfile`

  fasta file of tip sequences

`tree.file`

  tree file

`ancseq.file`

  ancestral sequence file, nexus format

`extraInfo`

  extra information

### Author(s)

Guangchuang Yu http://guangchuangyu.github.io

### See Also

paml_rst

[Package treeio version 1.2.2 Index]