Nnode.treedata          Nnode
as.treedata.phylo       as.treedata
drop.tip                drop.tip method
get.placements          get.placements
get.tree                get.tree
get.treetext            get.treetext method
getNodeNum              getNodeNum
is.ggtree               is.ggtree
isTip                   isTip
jplace-class            Class "jplace" This class stores phylogenetic
                        placements
label_branch_paml       label_branch_paml
mask                    mask
merge_tree              merge_tree
print.beastList         print
raxml2nwk               raxml2nwk
read.astral             read.astral
read.beast              read.beast
read.codeml             read.codeml
read.codeml_mlc         read.codeml_mlc
read.fasta              read.fasta
read.hyphy              read.hyphy
read.hyphy.seq          read.hyphy.seq
read.iqtree             read.iqtree
read.jplace             read.jplace
read.jtree              read.jtree
read.mega_tabular       read.mega_tabular
read.newick             read.newick
read.nhx                read.nhx
read.paml_rst           read.paml_rst
read.phylip             read.phylip
read.phylip.seq         read.phylip.seq
read.phylip.tree        read.phylip.tree
read.phyloT             read.phyloT
read.r8s                read.r8s
read.raxml              read.raxml
rename_taxa             rename_taxa
rescale_tree            rescale_tree
root.phylo              root
tree_subset             Subset tree objects by related nodes
write.beast             write.beast
write.jplace            write.jplace
write.jtree             write.jtree
