Package ‘treeio’

January 10, 2025

Title Base Classes and Functions for Phylogenetic Tree Input and
Output
Version 1.30.0
Description 'treeio' is an R package to make it easier to import and store phylogenetic tree with asso-
ciated data; and to link external data from different sources to phylogeny. It also supports export-
ing phylogenetic tree with heterogeneous associated data to a sin-
gle tree file and can be served as a platform for merging tree with associated data and convert-
ing file formats.
Depends R (>= 3.6.0)
Imports ape, dplyr, jsonlite, magrittr, methods, rlang, stats, tibble,
tidytree (>= 0.4.5), utils, yulab.utils (>= 0.1.6)
Suggests Biostrings, cli, ggplot2, ggtree, igraph, knitr, rmarkdown,
phangorn, prettydoc, purrr, testthat, tidyr, vroom, xml2, yaml
VignetteBuilder knitr
ByteCompile true
License Artistic-2.0
Encoding UTF-8

URL https://yulab-smu.top/contribution-tree-data/

BugReports https://github.com/YuLab-SMU/treeio/issues
biocViews Software, Annotation, Clustering, DataImport,
DataRepresentation, Alignment, MultipleSequenceAlignment,
Phylogenetics
RoxygenNote 7.3.2
git_url https://git.bioconductor.org/packages/treeio
git_branch RELEASE_3_20
git_last_commit c824ca4
git_last_commit_date 2024-10-29
Repository Bioconductor 3.20
Date/Publication 2025-01-09
Author Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>),
Tommy Tsan-Yuk Lam [ctb, ths],
Shuangbin Xu [ctb] (<https://orcid.org/0000-0003-3513-5362>),
Bradley Jones [ctb],

1
2 Contents

Casey Dunn [ctb],

Tyler Bradley [ctb],
Konstantinos Geles [ctb]
Maintainer Guangchuang Yu <[email protected]>

Contents
treeio-package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
as.treedata.phylo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
find.hclust . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
get.placements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
get.tree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
get.treetext . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
getNodeNum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
is.ggtree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
jplace-class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
label_branch_paml . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
mask . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
merge_tree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
print.treedataList . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
raxml2nwk . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
read.astral . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
read.beast . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
read.codeml . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
read.codeml_mlc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
read.fasta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
read.hyphy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
read.hyphy.seq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
read.iqtree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
read.jplace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
read.jtree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
read.mcmctree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
read.mega_tabular . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
read.newick . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
read.nextstrain.json . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
read.nhx . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
read.paml_rst . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
read.phylip . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
read.phylip.seq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
read.phylip.tree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
read.phyloxml . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
read.r8s . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
read.raxml . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
read.treeqza . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
read.treetime . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
reexports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
rename_taxa . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
rescale_tree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
spt . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
write.beast . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
write.beast.newick . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
treeio-package 3

write.jplace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
write.jtree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

Index 30

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

Description
’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.

Author(s)
Maintainer: Guangchuang Yu <[email protected]> (ORCID)
Other contributors:

• Tommy Tsan-Yuk Lam <[email protected]> [contributor, thesis advisor]

• Shuangbin Xu <[email protected]> (ORCID) [contributor]
• Bradley Jones <[email protected]> [contributor]
• Casey Dunn <[email protected]> [contributor]
• Tyler Bradley <[email protected]> [contributor]
• Konstantinos Geles <[email protected]> [contributor]

See Also
Useful links:

• https://yulab-smu.top/contribution-tree-data/
• Report bugs at https://github.com/YuLab-SMU/treeio/issues

as.treedata.phylo as.treedata

Description
convert phylo to treedata

Usage
## S3 method for class 'phylo'
as.treedata(tree, boot = NULL, ...)
4 find.hclust

Arguments
tree input tree, a phylo object
boot optional, can be bootstrap value from ape::boot.phylo
... additional parameters

Details
converting phylo object to treedata object

Author(s)
Guangchuang Yu

find.hclust find the hierarchical cluster analysis among the nodes of graph based
on the length of all the shortest paths in the graph.

Description
find the hierarchical cluster analysis among the nodes of graph based on the length of all the shortest
paths in the graph.

Usage
find.hclust(
x,
graph.mst = FALSE,
weights = NULL,
hclust.method = "average",
...
)

Arguments
x a igraph object
graph.mst logical whether obtain the minimum spanning tree first then find.hclust, default
is FALSE.
weights a numeric vector giving edge weights or a character. If this is NULL and the
graph has a weight edge attribute, then the attribute is used. If this is NA then no
weights are used even if the graph has a weight attribute. If this is a character,
the graph has the edge attribute which is numeric, then it will be used, default is
NULL.
hclust.method the agglomeration method to be used, This should be (an unambiguous abbrevi-
ation of) one of "ward.D", "ward.D2", "single", "complete", "average" (=
UPGMA), "mcquitty" (= WPGMA), "median" (= WPGMC) or "centroid"
(= UPGMC).
... additional parameters
get.placements 5

Value
hclust object

Examples
library(igraph)
set.seed(123)
g <- igraph::sample_gnp(100, .1) %>%
set_edge_attr(name='weight', value=abs(rnorm(E(.),3)))
tr1 <- find.hclust(g, weights = NA)
tr2 <- find.hclust(g)
tr3 <- find.hclust(g, graph.mst = TRUE)

get.placements get.placements

Description
access placement information

Usage
get.placements(tree, ...)

## S3 method for class 'jplace'

get.placements(tree, by = "best", ...)

Arguments
tree tree object
... additional parameters
by one of ’best’ and ’all’

Value
placement tibble

get.tree get.tree

Description
access phylo slot

Usage
get.tree(x, ...)
6 getNodeNum

Arguments
x tree object
... additional parameters

Value
phylo object

Author(s)
Guangchuang Yu

get.treetext get.treetext method

Description
access tree text (newick text) from tree object

Usage
get.treetext(object, ...)

Arguments
object treedata object
... additional parameter

Value
phylo object

getNodeNum getNodeNum

Description
calculate total number of nodes

Usage
getNodeNum(tree)

Nnode2(tree)

Arguments
tree tree object
is.ggtree 7

Value
number

Author(s)
Guangchuang Yu

Examples
getNodeNum(rtree(30))
Nnode2(rtree(30))

is.ggtree is.ggtree

Description
test whether input object is produced by ggtree function

Usage
is.ggtree(x)

Arguments
x object

Value
TRUE or FALSE

Author(s)
Guangchuang Yu

jplace-class Class "jplace" This class stores phylogenetic placements

Description
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
file tree file
placements reserve for jplace file to store placement information
info extra information, e.g. metadata, software version etc.
8 mask

Author(s)
Guangchuang Yu https://guangchuangyu.github.io

label_branch_paml label_branch_paml

Description
label branch for PAML to infer selection pressure using branch model

Usage
label_branch_paml(tree, node, label)

Arguments
tree phylo object
node node number
label label of branch, e.g. #1

Value
updated phylo object

Author(s)
Guangchuang Yu

mask mask

Description
site mask

Usage
mask(tree_object, field, site, mask_site = FALSE)

Arguments
tree_object tree object
field selected field
site site
mask_site if TRUE, site will be masked. if FALSE, selected site will not be masked, while
other sites will be masked.
merge_tree 9

Value
updated tree object

Author(s)
Guangchuang Yu

merge_tree merge_tree

Description
merge two tree object

Usage
merge_tree(obj1, obj2)

Arguments
obj1 tree object 1
obj2 tree object 2

Value
tree object

Author(s)
Guangchuang Yu

print.treedataList print

Description
print information of a list of treedata objects

Usage
## S3 method for class 'treedataList'
print(x, ...)

Arguments
x a list of treedata objects
... no used

Value
message
10 read.astral

raxml2nwk raxml2nwk

Description
convert raxml bootstrap tree to newick format

Usage
raxml2nwk(infile, outfile = "raxml.tree")

Arguments
infile input file
outfile output file

Value
newick file

Author(s)
Guangchuang Yu

read.astral read.astral

Description
parse ASTRAL output newick text

Usage
read.astral(file)

Arguments
file ASTRAL Newick file

Value
treedata object

Author(s)
Guangchuang Yu
read.beast 11

Examples
tt <- paste0(
"((species1,(species2,species3)'[pp1=0.75;pp2=0.24;pp3=0.01]':",
"1.2003685744180805)'[pp1=0.98;pp2=0.02;pp3=0]':0.9679599282730038,",
"((species4,species5)'[pp1=0.88;pp2=0.11;pp3=0.01]':1.2454851536484994))"
)
read.astral(textConnection(tt))

read.beast read.beast

Description
read beast/mrbayes/mega Nexus output
read beast/mrbayes/mega newick file format

Usage
read.beast(file, threads = 1, verbose = FALSE)

read.mrbayes(file, threads = 1, verbose = FALSE)

read.beast.newick(file, threads = 1, verbose = FALSE)

read.mega(file, threads = 1, verbose = FALSE)

Arguments
file newick file
threads number of threads for multithreading (default: 1)
verbose set TRUE to log progress (default: FALSE)

Value
treedata object
treedata object

Author(s)
Guangchuang Yu https://guangchuangyu.github.io
Bradley R Jones

Examples
file <- system.file("extdata/BEAST", "beast_mcc.tree", package="treeio")
read.beast(file)
file <- system.file("extdata/MrBayes", "Gq_nxs.tre", package="treeio")
read.mrbayes(file)
tr <- read.beast.newick(
textConnection(
'(a[&rate=1]:2,(b[&rate=1.1]:1,c[&rate=0.9]:1)[&rate=1]:1);'
)
)
12 read.codeml_mlc

read.codeml read.codeml

Description
read baseml output

Usage
read.codeml(rstfile, mlcfile, tree = "mlc", type = "Joint")

Arguments
rstfile rst file
mlcfile mlc file
tree one of ’mlc’ or ’rst’
type one of ’Marginal’ or ’Joint’

Value
A treedata object

Author(s)
Guangchuang Yu

Examples
rstfile <- system.file("extdata/PAML_Codeml", "rst", package="treeio")
mlcfile <- system.file("extdata/PAML_Codeml", "mlc", package="treeio")
read.codeml(rstfile, mlcfile)

read.codeml_mlc read.codeml_mlc

Description
read mlc file of codeml output

Usage
read.codeml_mlc(mlcfile)

Arguments
mlcfile mlc file

Value
A codeml_mlc object
read.fasta 13

Author(s)

Guangchuang Yu

Examples

mlcfile <- system.file("extdata/PAML_Codeml", "mlc", package="treeio")

read.codeml_mlc(mlcfile)

read.fasta read.fasta

Description

read FASTA file

Usage

read.fasta(fasta, type = "auto")

Arguments

fasta fasta file

type sequence type of the input file, one of ’NT’ or ’AA’. Default is ’auto’ and guess
the sequence type automatically

Details

This function supports both DNA or AA sequences

Value

DNAbin or AAbin object

Author(s)

Guangchuang Yu
14 read.hyphy.seq

read.hyphy read.hyphy

Description
read HYPHY output

Usage
read.hyphy(nwk, ancseq, tip.fasfile = NULL)

Arguments
nwk tree file in nwk format, one of hyphy output
ancseq ancestral sequence file in nexus format, one of hyphy output
tip.fasfile tip sequence file

Value
A hyphy object

Author(s)
Guangchuang Yu https://guangchuangyu.github.io

Examples
nwk <- system.file("extdata/HYPHY", "labelledtree.tree", package="treeio")
ancseq <- system.file("extdata/HYPHY", "ancseq.nex", package="treeio")
read.hyphy(nwk, ancseq)

read.hyphy.seq read.hyphy.seq

Description
parse sequences from hyphy output

Usage
read.hyphy.seq(file)

Arguments
file output of hyphy ancestral sequence inference; nexus format

Value
DNAbin object
read.iqtree 15

Author(s)
Guangchuang Yu

Examples
ancseq <- system.file("extdata/HYPHY", "ancseq.nex", package="treeio")
read.hyphy.seq(ancseq)

read.iqtree read.iqtree

Description
parse IQ-TREE output

Usage
read.iqtree(file)

Arguments
file IQ-TREE Newick text

Value
treedata object

Author(s)
Guangchuang Yu

read.jplace read.jplace

Description
read jplace file

Usage
read.jplace(file)

Arguments
file jplace file

Value
jplace instance
16 read.mcmctree

Author(s)
Guangchuang Yu

Examples
jp <- system.file("extdata", "sample.jplace", package="treeio")
read.jplace(jp)

read.jtree read.jtree

Description
Import tree data from jtree file, which is JSON-based text and probably output by write.jtree

Usage
read.jtree(file)

Arguments
file tree file

Value
treedata object

Author(s)
Guangchuang Yu

read.mcmctree read.mcmctree

Description
read MCMCTree output Tree

Usage
read.mcmctree(file, force.ultrametric = FALSE)

Arguments
file the output tree file of MCMCTree
force.ultrametric
logical whether convert the tree to be ultrametric, if it is not ultrametric, de-
fault is FALSE. When the tree is ultrametric, branch times will be calculated
automatically.
read.mega_tabular 17

Value
treedata object

Examples
file <- system.file("extdata/MCMCTree", "mcmctree_output.tree", package="treeio")
tr <- read.mcmctree(file)
tr

read.mega_tabular read.mega_tabular

Description
parse tabular output of MEGA

Usage
read.mega_tabular(file)

Arguments
file MEGA tabular file

Value
treedata object

Author(s)
Guangchuang Yu

read.newick read.newick

Description
read newick tree

Usage
read.newick(file, node.label = "label", ...)

Arguments
file newick file
node.label parse node label as ’label’ or ’support’ value
... additional parameter, passed to ’read.tree’
18 read.nhx

Value
phylo or treedata object

Author(s)
Guangchuang Yu

read.nextstrain.json read.nextstrain.json

Description
read.nextstrain.json

Usage
read.nextstrain.json(x)

Arguments
x the json tree file of auspice from nextstrain.

Value
treedata object

Author(s)
Shuangbin Xu

Examples
file1 <- system.file("extdata/nextstrain.json", "minimal_v2.json", package="treeio")
tr <- read.nextstrain.json(file1)
tr

read.nhx read.nhx

Description
read nhx tree file

Usage
read.nhx(file)

Arguments
file nhx file
read.paml_rst 19

Value

nhx object

Author(s)

Guangchuang Yu https://guangchuangyu.github.io

Examples

nhxfile <- system.file("extdata/NHX", "ADH.nhx", package="treeio")

read.nhx(nhxfile)

read.paml_rst read.paml_rst

Description

read rst file from paml (both baseml and codeml) output

Usage

read.paml_rst(rstfile, type = "Joint")

Arguments

rstfile rst file

type one of ’Marginal’ or ’Joint’

Value

A treedata object

Author(s)

Guangchuang Yu https://guangchuangyu.github.io

Examples

rstfile <- system.file("extdata/PAML_Baseml", "rst", package="treeio")

read.paml_rst(rstfile)
20 read.phylip.seq

read.phylip read.phylip

Description
parsing phylip tree format

Usage
read.phylip(file)

Arguments
file phylip file

Value
an instance of ’phylip’

Author(s)
Guangchuang Yu

Examples
phyfile <- system.file("extdata", "sample.phy", package="treeio")
read.phylip(phyfile)

read.phylip.seq read.phylip.seq

Description
read aligned sequences from phylip format

Usage
read.phylip.seq(file)

Arguments
file phylip file, currently only sequential format is supported

Value
DNAbin object

Author(s)
Guangchuang Yu
read.phylip.tree 21

References
http://evolution.genetics.washington.edu/phylip/doc/sequence.html

read.phylip.tree read.phylip.tree

Description
parse tree from phylip file

Usage
read.phylip.tree(file)

Arguments
file phylip file

Value
phylo or multiPhylo object

Author(s)
Guangchuang Yu

read.phyloxml read.phyloxml

Description
read.phyloxml

Usage
read.phyloxml(file)

Arguments
file phyloxml file

Value
treedata class or treedataList class

Examples
xmlfile1 <- system.file("extdata/phyloxml", "test_x2.xml", package="treeio")
px1 <- read.phyloxml(xmlfile1)
px1
xmlfile2 <- system.file("extdata/phyloxml", "phyloxml_examples.xml", package="treeio")
px2 <- read.phyloxml(xmlfile2)
px2
22 read.raxml

read.r8s read.r8s

Description
parse output from r8s

Usage
read.r8s(file)

Arguments
file r8s output log file

Value
multiPhylo object

Author(s)
Guangchuang Yu

Examples
read.r8s(system.file("extdata/r8s", "H3_r8s_output.log", package="treeio"))

read.raxml read.raxml

Description
parse RAxML bootstrapping analysis output

Usage
read.raxml(file)

Arguments
file RAxML bootstrapping analysis output

Value
treedata object

Author(s)
Guangchuang Yu
read.treeqza 23

Examples

raxml_file <- system.file("extdata/RAxML", "RAxML_bipartitionsBranchLabels.H3", package="treeio")

read.raxml(raxml_file)

read.treeqza read.treeqza

Description

read.treeqza

Usage

read.treeqza(treeqza, node.label = "label", ...)

Arguments

treeqza the qiime2 output file contained tree file.

node.label parse node label as ’label’ or ’support’ value.
... additional parameter, passed to ’read.tree’.

Value

phylo tree object or treedata object when node.label was parsed ’support’.

Examples

qzafile1 <- system.file("extdata/qiime2treeqza", "fasttree-tree.qza", package="treeio")

qzafile2 <- system.file("extdata/qiime2treeqza", "iqt-tree.qza", package="treeio")
qzafile3 <- system.file("extdata/qiime2treeqza", "raxml-cat-tree.qza", package="treeio")
tr1 <- read.treeqza(qzafile1)
tr1
tr2 <- read.treeqza(qzafile2)
tr2
tr3 <- read.treeqza(qzafile3)
tr3
# parse node label as 'support' value.
qzafile4 <- system.file("extdata/qiime2treeqza", "raxml-cat-bootstrap-tree.qza", package="treeio")
tr4 <- read.treeqza(qzafile4, node.label="support")
tr4
24 reexports

read.treetime read.timetree

Description

read timetree output

Usage

read.treetime(file)

read.timetree(file)

Arguments

file the output tree file of timetree

Value

treedata object

reexports Objects exported from other packages

Description

These objects are imported from other packages. Follow the links below to see their documentation.

ape as.phylo, is.rooted, Nnode, Ntip, read.nexus, read.tree, root, rtree, write.nexus,
write.tree
dplyr full_join, inner_join
magrittr %<>%, %>%
rlang .data
tibble as_tibble, tibble
tidytree ancestor, as.phylo, as.treedata, child, drop.tip, get.data, get.fields, isTip,
MRCA, nodeid, nodelab, offspring, parent, rootnode, treedata
rename_taxa 25

rename_taxa rename_taxa

Description
rename tip label of phylogenetic tree

Usage
rename_taxa(tree, data, key = 1, value = 2)

Arguments
tree tree object, either treedata or phylo
data data frame
key column in data that match tip label (use 1st column by default)
value column in data for rename tip label (use 2nd column by default)

Value
tree object

Author(s)
Guangchuang Yu

Examples
tree <- rtree(3)
d <- data.frame(old = paste0('t', 1:3), new = LETTERS[1:3])
rename_taxa(tree, d)
rename_taxa(tree, d, old, new)

rescale_tree rescale_tree

Description
rescale branch length of tree object

Usage
rescale_tree(tree_object, branch.length)

Arguments
tree_object tree object
branch.length numerical features (e.g. dN/dS)
26 spt

Value

update tree object

Author(s)

Guangchuang Yu

spt spt method

Description

spt method

Usage

spt(x, from, to, weights = NULL, ...)

Arguments

x a igraph object
from a specific node of network.
to other nodes of the network, length of it must be larger than 2.
weights a numeric vector giving edge weights or a character. If this is NULL and the
graph has a weight edge attribute, then the attribute is used. If this is NA then no
weights are used even if the graph has a weight attribute. If this is a character,
the graph has the edge attribute which is numeric, then it will be used, default is
NULL.
... additional parameters

Value

phylo object

Examples
library(igraph)
set.seed(123)
g <- igraph::sample_gnp(100, .1) %>%
set_edge_attr(name='weight', value=abs(rnorm(E(.),3)))
tr1 <- spt(g, from = 6, to=V(g), weights = 'weight')
tr1
tr2 <- spt(g, from = 6, to = V(g), weights = NA)
tr2
write.beast 27

write.beast write.beast

Description
Export treedata object to BEAST NEXUS file. This function was adopted and modified from
ape::write.nexus

Usage
write.beast(treedata, file = "", translate = TRUE, tree.name = NULL)

Arguments
treedata treedata object, list of treedata, phylo, or list of phylo
file output file. If file = "", print the output content on screen
translate whether to translate taxa labels
tree.name names of the trees, NULL to use existing tree names

Value
output file or file content on screen

Author(s)
Guangchuang Yu

Examples
nhxfile <- system.file("extdata/NHX", "phyldog.nhx", package="treeio")
nhx <- read.nhx(nhxfile)
write.beast(nhx)

write.beast.newick write.beast.newick

Description
Export treedata object to BEAST Newick file. This is useful for making BEAST starting trees
with metadata

Usage
write.beast.newick(
treedata,
file = "",
append = FALSE,
digits = 10,
tree.prefix = ""
)
28 write.jplace

Arguments
treedata treedata object
file output file. If file = "", print the output content on screen
append logical. Only used if the argument ’file’ is the name of file (and not a connec-
tion or "|cmd"). If ’TRUE’ output will be appended to ’file’; otherwise, it will
overwrite the contents of file.
digits integer, the indicating the number of decimal places, default is 10.
tree.prefix character the tree prefix, default is "".

Value
output file or file content on screen

Author(s)
Guangchuang Yu

Examples
nhxfile <- system.file("extdata/NHX", "phyldog.nhx", package="treeio")
nhx <- read.nhx(nhxfile)
write.beast.newick(nhx)

write.jplace write.jplace

Description
Export jplace object to jplace file.

Usage
write.jplace(x, outfile)

Arguments
x a jplace object.
outfile the output file name

Examples
jp <- system.file("extdata", "sample.jplace", package="treeio")
tr1 <- read.jplace(jp)
outfile <- tempfile()
write.jplace(tr1, outfile)
tr2 <- read.jplace(outfile)
tr2
write.jtree 29

write.jtree write.jtree

Description
Export treedata object to json tree file

Usage
write.jtree(treedata, file = "")

Arguments
treedata treedata object
file output file. If file = "", print the output content on screen

Value
output file or file content on screen

Author(s)
Guangchuang Yu
Index

∗ classes is.rooted (reexports), 24

jplace-class, 7 isTip, 24
∗ internal isTip (reexports), 24
reexports, 24
treeio-package, 3 jplace-class, 7
.data, 24
.data (reexports), 24 label_branch_paml, 8
%<>% (reexports), 24
mask, 8
%>% (reexports), 24
merge_tree, 9
%<>%, 24
MRCA, 24
%>%, 24
MRCA (reexports), 24
ancestor, 24
Nnode, 24
ancestor (reexports), 24
Nnode (reexports), 24
as.phylo, 24
Nnode2 (getNodeNum), 6
as.phylo (reexports), 24
nodeid, 24
as.treedata, 24
nodeid (reexports), 24
as.treedata (reexports), 24
nodelab, 24
as.treedata.phylo, 3
nodelab (reexports), 24
as_tibble, 24
Ntip, 24
as_tibble (reexports), 24
Ntip (reexports), 24
child, 24
offspring, 24
child (reexports), 24
offspring (reexports), 24
drop.tip, 24
drop.tip (reexports), 24 parent, 24
parent (reexports), 24
find.hclust, 4 print.treedataList, 9
full_join, 24
full_join (reexports), 24 raxml2nwk, 10
read.astral, 10
get.data, 24 read.beast, 11
get.data (reexports), 24 read.codeml, 12
get.fields, 24 read.codeml_mlc, 12
get.fields (reexports), 24 read.fasta, 13
get.placements, 5 read.hyphy, 14
get.tree, 5 read.hyphy.seq, 14
get.treetext, 6 read.iqtree, 15
getNodeNum, 6 read.jplace, 15
read.jtree, 16
inner_join, 24 read.mcmctree, 16
inner_join (reexports), 24 read.mega (read.beast), 11
is.ggtree, 7 read.mega_tabular, 17
is.rooted, 24 read.mrbayes (read.beast), 11

30
INDEX 31

read.newick, 17
read.nextstrain.json, 18
read.nexus, 24
read.nexus (reexports), 24
read.nhx, 18
read.paml_rst, 19
read.phylip, 20
read.phylip.seq, 20
read.phylip.tree, 21
read.phyloxml, 21
read.r8s, 22
read.raxml, 22
read.timetree (read.treetime), 24
read.tree, 24
read.tree (reexports), 24
read.treeqza, 23
read.treetime, 24
reexports, 24
rename_taxa, 25
rescale_tree, 25
root, 24
root (reexports), 24
rootnode, 24
rootnode (reexports), 24
rtree, 24
rtree (reexports), 24

spt, 26

tibble, 24
tibble (reexports), 24
treedata, 24
treedata (reexports), 24
treeio (treeio-package), 3
treeio-package, 3

write.beast, 27
write.beast.newick, 27
write.jplace, 28
write.jtree, 29
write.nexus, 24
write.nexus (reexports), 24
write.tree, 24
write.tree (reexports), 24