# Base Classes and Functions for Phylogenetic Tree Input and Output

## Documentation for package ‘treeio’ version 1.0.2

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

## Help Pages

as.treedata | as.treedata
as.treedata.phylo | 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
drop.tip,phylo | drop.tip method
drop.tip,treedata | drop.tip method
drop.tip-method | drop.tip method
get.fields | get.fields method
get.fields-method | get.fields method
get.fields-method | Class "jplace" This class stores information of jplace file.
get.placements | get.placements method
get.placements-method | get.placements method
get.placements-method | Class "jplace" This class stores information of jplace file.
get.subs | get.subs method
get.subs-method | get.subs method
get.tipseq | get.tipseq method
get.tipseq-method | get.tipseq method
get.tree | get.tree method
get.tree,beast | get.tree method
get.tree-method | Class "beast" This class stores information of beast output
get.tree-method | get.tree method
get.treeinfo-method | Class "jplace" This class stores information of jplace file.
get.treetext | get.treetext method
get.treetext-method | get.treetext method
get.treetext-method | Class "jplace" This class stores information of jplace file.
getNodeNum | getNodeNum
getRoot | getRoot
groupClade | groupClade method
groupClade-method | groupClade method
groupOTU | groupOTU method
groupOTU-method | 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
Nnode | Nnode
Nnode2 | getNodeNum
Ntip | Ntip
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'
phylip-class | Class "phylip" This class stores phylip tree(s)
phyPML | treeAnno.pml
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
set.subs-method | Class "paml_rst" This class stores information of rst file from PAML output
set.subs<--method | Class "paml_rst" This class stores information of rst file from PAML output
show | show method
show-method | Class "jplace" This class stores information of jplace file.
show-method | show method
taxa_rename | taxa_rename
treedata-class | Class "treedata" This class stores phylogenetic tree with associated data
write.jplace | write.jplace