Nnode                   Nnode
Ntip                    Ntip
as.treedata             as.treedata
beast-class             Class "beast" This class stores information of
                        beast output
codeml-class            Class "codeml" This class stores information of
                        output from codeml
codeml_mlc-class        Class "codeml_mlc" This class stores
                        information of mlc file frm codeml output
drop.tip                drop.tip method
get.fields              get.fields method
get.placements          get.placements method
get.subs                get.subs method
get.tipseq              get.tipseq method
get.tree                get.tree method
get.treetext            get.treetext method
getNodeNum              getNodeNum
getRoot                 getRoot
groupClade              groupClade method
groupOTU                groupOTU method
groupOTU.phylo          groupOTU.phylo
hyphy-class             Class "hyphy" This class stores information of
                        HYPHY output
is.ggtree               is.ggtree
jplace-class            Class "jplace" This class stores information of
                        jplace file.
label_branch_paml       label_branch_paml
mask                    mask
merge_tree              merge_tree
paml_rst-class          Class "paml_rst" This class stores information
                        of rst file from PAML output
phangorn-class          Class "phangorn" This class stores ancestral
                        sequences inferred from 'phangorn'
phyPML                  treeAnno.pml
phylip-class            Class "phylip" This class stores phylip tree(s)
pmlToSeq                pmlToSeq
print.beastList         print
r8s-class               Class "r8s" This class stores output info from
                        r8s
raxml2nwk               raxml2nwk
read.baseml             read.baseml
read.beast              read.beast
read.codeml             read.codeml
read.codeml_mlc         read.codeml_mlc
read.hyphy              read.hyphy
read.jplace             read.jplace
read.newick             read.newick
read.nhx                read.nhx
read.paml_rst           read.paml_rst
read.phylip             read.phylip
read.phyloT             read.phyloT
read.r8s                read.r8s
read.raxml              read.raxml
show,beast-method       show method
taxa_rename             taxa_rename
treedata-class          Class "treedata" This class stores phylogenetic
                        tree with associated data
write.jplace            write.jplace
