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

Description

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

Slots

fields

availabel attributes

treetext

tree text

phylo

phylo object

seq_type

one of "NT" and "AA"

tip_seq

sequences of tips

marginal_ancseq

Marginal reconstruction of ancestral sequences

joint_ancseq

Joint reconstruction of ancestral sequences

marginal_subs

sequence substitutions based on marginal_ancseq

joint_subs

sequence substitutions based on joint_ancseq

marginal_AA_subs

Amino acid sequence substitutions based on marginal_ancseq

joint_AA_subs

Amino acid sequence substitutions based on joint_ancseq

rstfile

rst file

extraInfo

extra information

Author(s)

Guangchuang Yu http://guangchuangyu.github.io

See Also

codeml codeml_mlc