Base Classes and Functions for Phylogenetic Tree Input and Output


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Documentation for package ‘treeio’ version 1.2.2

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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