# Base Classes and Functions for Phylogenetic Tree Input and Output

## Documentation for package ‘treeio’ version 1.6.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

as.treedata.phylo | as.treedata
drop.tip | drop.tip method
drop.tip,phylo | drop.tip method
drop.tip,treedata | drop.tip method
drop.tip-method | drop.tip method
get.placements | get.placements
get.placements.jplace | get.placements
get.tree | get.tree
get.treetext | get.treetext method
get.treetext-method | 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
Nnode.treedata | Nnode
Nnode2 | getNodeNum
phyPML | treeAnno.pml
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.mrbayes | read.beast
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
taxa_rename | taxa_rename
tree_subset | Subset tree objects by related nodes
tree_subset.phylo | Subset tree objects by related nodes
tree_subset.treedata | Subset tree objects by related nodes
write.beast | write.beast
write.jplace | write.jplace
write.jtree | write.jtree