All functions

Nnode(<treedata>)

Nnode

as.treedata(<phylo>) as.treedata(<pml>)

as.treedata

read.beast() read.mrbayes() read.mega()

read.beast

drop.tip() drop.tip()

drop.tip method

get.placements()

get.placements

get.tree()

get.tree

get.treetext()

get.treetext method

getNodeNum() Nnode2()

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(<treedataList>)

print

raxml2nwk()

raxml2nwk

read.jtree()

read.jtree

read.astral()

read.astral

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.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.phyloxml()

read.phyloxml

read.r8s()

read.r8s

read.raxml()

read.raxml

rename_taxa()

rename_taxa

rescale_tree()

rescale_tree

root(<phylo>) root(<treedata>)

root

tree_subset()

Subset tree objects by related nodes

write.jtree()

write.jtree

write.beast()

write.beast