Package treeio. April 1, 2018

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1 Package treeio April 1, 2018 Title Base Classes and Functions for Phylogenetic Tree Input and Output Version Base classes and functions for parsing and exporting phylogenetic trees. 'treeio' supports parsing analysis findings from commonly used software packages, allows linking external data to phylogeny and merging tree data obtained from different sources. It also supports exporting phylogenetic tree with heterogeneous associated data to a single tree. Depends R (>= 3.4.0) Imports ape, dplyr, jsonlite, magrittr, methods, rvcheck, tibble, tidytree (>= 0.1.7) Suggests ggplot2, ggtree, knitr, prettydoc, testthat, tidyr VignetteBuilder knitr ByteCompile true License Artistic-2.0 URL BugReports Encoding UTF-8 LazyData true biocviews Software, Annotation, Clustering, DataImport, DataRepresentation, Alignment, MultipleSequenceAlignment RoxygenNote Author Guangchuang Yu [aut, cre] (< Tommy Tsan-Yuk Lam [ctb, ths], Casey Dunn [ctb], Bradley Jones [ctb] Maintainer Guangchuang Yu <guangchuangyu@gmail.com> R topics documented: as.treedata.phylo drop.tip get.placements get.tree get.treetext

2 2 as.treedata.phylo getnodenum is.ggtree jplace-class label_branch_paml mask merge_tree Nnode.treedata phypml print.beastlist raxml2nwk read.beast read.codeml read.codeml_mlc read.fasta read.hyphy read.hyphy.seq read.jplace read.jtree read.newick read.nhx read.paml_rst read.phylip read.phylip.seq read.phylip.tree read.phylot read.r8s read.raxml taxa_rename write.beast write.jplace write.jtree Index 22 as.treedata.phylo as.treedata convert phylo to treedata ## S3 method for class 'phylo' as.treedata(tree, boot = NULL,...) tree boot input tree, a phylo object optional, can be bootstrap value from ape::boot.phylo... additional parameters

3 drop.tip 3 Details converting phylo object to treedata object drop.tip drop.tip method drop.tip method drop.tip(object, tip,...) drop.tip(object, tip,...) ## S4 method for signature 'phylo' drop.tip(object, tip,...) object tip A treedata or phylo object a vector of mode numeric or character specifying the tips to delete... additional parameters updated object Source Casey Dunn and Guangchuang Yu drop.tip for phylo object is a wrapper method of ape::drop.tip from the ape package. The documentation you should read for the drop.tip function can be found here: drop.tip See Also drop.tip nhx <- system.("extdata/nhx", "ADH.nhx", package="treeio") nhx <- read.nhx(nhx) drop.tip(nhx, c("adh2", "ADH1"))

4 4 get.tree get.placements get.placements access placement information get.placements(tree,...) ## S3 method for class 'jplace' get.placements(tree, by = "best",...) tree tree object... additional parameters by placement tibble one of best and all get.tree get.tree access phylo slot get.tree(x,...) x tree object... additional parameters phylo object

5 get.treetext 5 get.treetext get.treetext method access tree text (newick text) from tree object get.treetext method get.treetext(object,...) ## S4 method for signature 'treedata' get.treetext(object) object treedata object... additional parameter phylo object getnodenum getnodenum calculate total number of nodes getnodenum(tree) Nnode2(tree) tree tree object number Guangchuang Yu

6 6 jplace-class getnodenum(rtree(30)) Nnode2(rtree(30)) is.ggtree is.ggtree test whether input object is produced by ggtree function is.ggtree(x) x object TRUE or FALSE jplace-class Class "jplace" This class stores phylogenetic placements Class "jplace" This class stores phylogenetic placements Slots phylo phylo object for tree structure treetext newick tree string data associated data extrainfo extra information, reserve for merge_tree tree placements reserve for jplace to store placement information info extra information, e.g. metadata, software version etc.

7 label_branch_paml 7 label_branch_paml label_branch_paml label branch for PAML to infer selection pressure using branch model label_branch_paml(tree, node, label) tree phylo object node node number label label of branch, e.g. #1 updated phylo object mask mask site mask mask(tree_object, field, site, mask_site = FALSE) tree_object field site mask_site tree object selected field site if TRUE, site will be masked. if FALSE, selected site will not be masked, while other sites will be masked. updated tree object Guangchuang Yu

8 8 Nnode.treedata merge_tree merge_tree merge two tree object merge_tree(obj1, obj2) obj1 tree object 1 obj2 tree object 2 tree object Guangchuang Yu Nnode.treedata Nnode number of nodes ## S3 method for class 'treedata' Nnode(phy, internal.only = TRUE,...) phy internal.only treedata object whether only count internal nodes... additional parameters number of nodes

9 phypml 9 Nnode(rtree(30)) phypml treeanno.pml tree annotation of sequence substitution by comparing to parent node phypml(pmltree, type = "ml") pmltree type tree in pml object, output of phangorn::optim.pml one of ml and bayes for inferring ancestral sequences phangorn object Yu Guangchuang print.beastlist print print information of a list of beast trees ## S3 method for class 'beastlist' print(x,...) x... no used message a list of beast object

10 10 read.beast raxml2nwk raxml2nwk convert raxml bootstrap tree to newick format raxml2nwk(in, out = "raxml.tree") in out input output newick Guangchuang Yu read.beast read.beast read beast output read.beast() read.mrbayes() beast beast object Guangchuang Yu <- system.("extdata/beast", "beast_mcc.tree", package="treeio") read.beast()

11 read.codeml 11 read.codeml read.codeml read baseml output read.codeml(rst, mlc, tree = "mlc", type = "Joint") rst mlc tree type rst mlc one of mlc or rst one of Marginal or Joint A treedata object Guangchuang Yu rst <- system.("extdata/paml_codeml", "rst", package="treeio") mlc <- system.("extdata/paml_codeml", "mlc", package="treeio") read.codeml(rst, mlc) read.codeml_mlc read.codeml_mlc read mlc of codeml output read.codeml_mlc(mlc) mlc mlc A codeml_mlc object

12 12 read.hyphy ygc mlc <- system.("extdata/paml_codeml", "mlc", package="treeio") read.codeml_mlc(mlc) read.fasta read.fasta read FASTA read.fasta(fasta) fasta fasta Details This function supports both DNA or AA sequences DNAbin or AAbin object read.hyphy read.hyphy read HYPHY output read.hyphy(nwk, ancseq, tip.fas = NULL) nwk ancseq tip.fas tree in nwk format, one of hyphy output ancestral sequence in nexus format, one of hyphy output tip sequence

13 read.hyphy.seq 13 A hyphy object Guangchuang Yu nwk <- system.("extdata/hyphy", "labelledtree.tree", package="treeio") ancseq <- system.("extdata/hyphy", "ancseq.nex", package="treeio") read.hyphy(nwk, ancseq) read.hyphy.seq read.hyphy.seq parse sequences from hyphy output read.hyphy.seq() output of hyphy ancestral sequence inference; nexus format DNAbin object ancseq <- system.("extdata/hyphy", "ancseq.nex", package="treeio") read.hyphy.seq(ancseq)

14 14 read.jtree read.jplace read.jplace read jplace read.jplace() jplace jplace instance ygc jp <- system.("extdata", "sample.jplace", package="treeio") read.jplace(jp) read.jtree read.jtree Import tree data from jtree, which is JSON-based text and probably output by write.jtree read.jtree() tree treedata object

15 read.newick 15 read.newick read.newick read newick tree read.newick(, node.label = "label",...) newick node.label parse node label as label or support value... additional parameter, passed to read.tree phylo or treedata object read.nhx read.nhx read nhx tree read.nhx() nhx nhx object Guangchuang Yu nhx <- system.("extdata/nhx", "ADH.nhx", package="treeio") read.nhx(nhx)

16 16 read.phylip read.paml_rst read.paml_rst read rst from paml (both baseml and codeml) output read.paml_rst(rst, type = "Joint") rst type rst one of Marginal or Joint A treedata object Guangchuang Yu rst <- system.("extdata/paml_baseml", "rst", package="treeio") read.paml_rst(rst) read.phylip read.phylip parsing phylip tree format read.phylip() phylip an instance of phylip Guangchuang Yu

17 read.phylip.seq 17 phy <- system.("extdata", "sample.phy", package="treeio") read.phylip(phy) read.phylip.seq read.phylip.seq read aligned sequences from phylip format read.phylip.seq() phylip, currently only sequential format is supported DNAbin object References read.phylip.tree read.phylip.tree parse tree from phylip read.phylip.tree() phylip phylo or multiphylo object

18 18 read.r8s read.phylot read.phylot parse output from phylot read.phylot(,...) newick tree... additional parameters to read.tree phylo object References read.r8s read.r8s parse output from r8s read.r8s() r8s output log multiphylo object Guangchuang Yu

19 read.raxml 19 read.r8s(system.("extdata/r8s", "H3_r8s_output.log", package="treeio")) read.raxml read.raxml parse RAxML bootstrapping analysis output read.raxml() RAxML bootstrapping analysis output raxml object Guangchuang Yu raxml_ <- system.("extdata/raxml", "RAxML_bipartitionsBranchLabels.H3", package="treeio") read.raxml(raxml_) taxa_rename taxa_rename rename taxa taxa_rename(tree, name) tree name tree object a two column data.frame contains original name in 1st column and new name in 2nd column updated tree object with new taxa name

20 20 write.jplace write.beast write.beast Export treedata object to BEAST NEXUS. This function was adopted and modified from ape::write.nexus write.beast(treedata, = "", translate = TRUE, tree.name = "UNTITLED") treedata translate tree.name treedata object output. If = "", print the output content on screen whether translate taxa labels name of the tree output or content on screen nhx <- system.("extdata/nhx", "phyldog.nhx", package="treeio") nhx <- read.nhx(nhx) write.beast(nhx) write.jplace write.jplace generate jplace write.jplace(nwk, data, out)

21 write.jtree 21 nwk data out tree in newick format annotation data jplace output jplace ygc write.jtree write.jtree Export treedata object to json tree write.jtree(treedata, = "") treedata treedata object output. If = "", print the output content on screen output or content on screen

22 Index Topic classes jplace-class, 6 as.treedata.phylo, 2 drop.tip, 3, 3 drop.tip,phylo (drop.tip), 3 drop.tip,phylo-method (drop.tip), 3 drop.tip,treedata (drop.tip), 3 drop.tip,treedata-method (drop.tip), 3 get.placements, 4 get.tree, 4 get.treetext, 5 get.treetext,treedata-method (get.treetext), 5 getnodenum, 5 read.paml_rst, 16 read.phylip, 16 read.phylip.seq, 17 read.phylip.tree, 17 read.phylot, 18 read.r8s, 18 read.raxml, 19 taxa_rename, 19 write.beast, 20 write.jplace, 20 write.jtree, 21 is.ggtree, 6 jplace-class, 6 label_branch_paml, 7 mask, 7 merge_tree, 8 Nnode.treedata, 8 Nnode2 (getnodenum), 5 phypml, 9 print.beastlist, 9 raxml2nwk, 10 read.beast, 10 read.codeml, 11 read.codeml_mlc, 11 read.fasta, 12 read.hyphy, 12 read.hyphy.seq, 13 read.jplace, 14 read.jtree, 14 read.mrbayes (read.beast), 10 read.newick, 15 read.nhx, 15 22