Package: treeio 1.33.0

Guangchuang Yu

treeio: Base Classes and Functions for Phylogenetic Tree Input and Output

'treeio' is an R package to make it easier to import and store phylogenetic tree with associated data; and to link external data from different sources to phylogeny. It also supports exporting phylogenetic tree with heterogeneous associated data to a single tree file and can be served as a platform for merging tree with associated data and converting file formats.

Authors:Guangchuang Yu [aut, cre], Tommy Tsan-Yuk Lam [ctb, ths], Shuangbin Xu [ctb], Bradley Jones [ctb], Casey Dunn [ctb], Tyler Bradley [ctb], Konstantinos Geles [ctb]

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treeio.pdf |treeio.html✨
treeio/json (API)
NEWS

# Install 'treeio' in R:
install.packages('treeio', repos = c('https://packages.ropensci.org', 'https://cloud.r-project.org'))

Reviews:rOpenSci Software Review #179

Bug tracker:https://github.com/yulab-smu/treeio/issues

On BioConductor:treeio-1.33.0(bioc 3.22)treeio-1.32.0(bioc 3.21)

softwareannotationclusteringdataimportdatarepresentationalignmentmultiplesequencealignmentphylogeneticsexporterparserphylogenetic-trees

12.42 score 102 stars 127 packages 1.5k scripts 76 exports 31 dependencies

Last updated 2 months agofrom:f5a6dec082 (on devel). Checks:10 OK. Indexed: yes.

TargetResultTotal time
pkgdown docsOK295
source / vignettesOK254
linux-devel-x86_64OK249
linux-release-x86_64OK225
macos-release-arm64OK106
macos-oldrel-arm64OK140
windows-develOK99
windows-releaseOK122
windows-oldrelOK109
wasm-releaseOK278

Exports:.data%<>%%>%ancestoras_tibbleas.phyloas.treedatachilddrop.tipfind.hclustfull_joinget.dataget.fieldsget.placementsget.treeget.treetextgetNodeNuminner_joinis.ggtreeis.rootedisTiplabel_branch_pamlmaskmerge_treeMRCANnodeNnode2nodeidnodelabNtipoffspringparentraxml2nwkread.astralread.beastread.beast.newickread.codemlread.codeml_mlcread.fastaread.hyphyread.hyphy.seqread.iqtreeread.jplaceread.jtreeread.mcmctreeread.megaread.mega_tabularread.mrbayesread.newickread.nextstrain.jsonread.nexusread.nhxread.paml_rstread.phylipread.phylip.seqread.phylip.treeread.phyloxmlread.r8sread.raxmlread.treeread.treeqzaread.treetimerename_taxarescale_treerootrootnodertreespttibbletreedatawrite.beastwrite.beast.newickwrite.jplacewrite.jtreewrite.nexuswrite.tree

Dependencies:apeclicpp11digestdplyrfansifsgenericsgluejsonlitelatticelazyevallifecyclemagrittrnlmepillarpkgconfigpurrrR6Rcpprlangstringistringrtibbletidyrtidyselecttidytreeutf8vctrswithryulab.utils

treeio: Base Classes and Functions for Phylogenetic Tree Input and Output

Guangchuang Yu School of Basic Medical Sciences, Southern Medical University

Rendered fromtreeio.Rmdusingknitr::rmarkdownon May 29 2025.

Last update: 2023-11-29
Started: 2016-12-06

Readme and manuals

Help Manual

Help pageTopics
as.treedataas.treedata.phylo
find the hierarchical cluster analysis among the nodes of graph based on the length of all the shortest paths in the graph.find.hclust
get.placementsget.placements get.placements.jplace
get.treeget.tree
get.treetext methodget.treetext
getNodeNumgetNodeNum Nnode2
is.ggtreeis.ggtree
Class "jplace" This class stores phylogenetic placementsjplace-class
label_branch_pamllabel_branch_paml
maskmask
merge_treemerge_tree
printprint.treedataList
raxml2nwkraxml2nwk
read.astralread.astral
read.beastread.beast read.beast.newick read.mega read.mrbayes
read.codemlread.codeml
read.codeml_mlcread.codeml_mlc
read.fastaread.fasta
read.hyphyread.hyphy
read.hyphy.seqread.hyphy.seq
read.iqtreeread.iqtree
read.jplaceread.jplace
read.jtreeread.jtree
read.mcmctreeread.mcmctree
read.mega_tabularread.mega_tabular
read.newickread.newick
read.nextstrain.jsonread.nextstrain.json
read.nhxread.nhx
read.paml_rstread.paml_rst
read.phylipread.phylip
read.phylip.seqread.phylip.seq
read.phylip.treeread.phylip.tree
read.phyloxmlread.phyloxml
read.r8sread.r8s
read.raxmlread.raxml
read.treeqzaread.treeqza
read.timetreeread.timetree read.treetime
rename_taxarename_taxa
rescale_treerescale_tree
spt methodspt
write.beastwrite.beast
write.beast.newickwrite.beast.newick
write.jplacewrite.jplace
write.jtreewrite.jtree