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