as.treedata.phylo       as.treedata
find.hclust             find the hierarchical cluster analysis among
                        the nodes of graph based on the length of all
                        the shortest paths in the graph.
get.placements          get.placements
get.tree                get.tree
get.treetext            get.treetext method
getNodeNum              getNodeNum
is.ggtree               is.ggtree
jplace-class            Class "jplace" This class stores phylogenetic
                        placements
label_branch_paml       label_branch_paml
mask                    mask
merge_tree              merge_tree
print.treedataList      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.mcmctree           read.mcmctree
read.mega_tabular       read.mega_tabular
read.newick             read.newick
read.nextstrain.json    read.nextstrain.json
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.phyloxml           read.phyloxml
read.r8s                read.r8s
read.raxml              read.raxml
read.treeqza            read.treeqza
rename_taxa             rename_taxa
rescale_tree            rescale_tree
spt                     spt method
write.beast             write.beast
write.beast.newick      write.beast.newick
write.jplace            write.jplace
write.jtree             write.jtree
