write.beast: write.beast
In treeio: Base Classes and Functions for Phylogenetic Tree Input and Output

Description Usage Arguments Value Author(s) Examples

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

1	write.beast(treedata, file = "", translate = TRUE, tree.name = "UNTITLED")

`treedata`	`treedata` object
`file`	output file. If file = "", print the output content on screen
`translate`	whether translate taxa labels
`tree.name`	name of the tree

output file or file content on screen

Guangchuang Yu

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

Registered S3 method overwritten by 'treeio':
  method     from
  root.phylo ape 
treeio v1.14.3  For help: https://yulab-smu.top/treedata-book/

If you use treeio in published research, please cite:

LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR Jones, T Bradley, H Zhu, Y Guan, Y Jiang, G Yu. treeio: an R package for phylogenetic tree input and output with richly annotated and associated data. Molecular Biology and Evolution 2020, 37(2):599-603. doi: 10.1093/molbev/msz240

#NEXUS
[R-package treeio, Mon Dec 21 06:10:01 2020]

BEGIN TAXA;
	DIMENSIONS NTAX = 16;
	TAXLABELS
		Prayidae_D27SS7@2825365
		Kephyes_ovata@2606431
		Chuniphyes_multidentata@1277217
		Apolemia_sp_@1353964
		Bargmannia_amoena@263997
		Bargmannia_elongata@946788
		Physonect_sp_@2066767
		Stephalia_dilata@2960089
		Frillagalma_vityazi@1155031
		Resomia_ornicephala@3111757
		Lychnagalma_utricularia@2253871
		Nanomia_bijuga@717864
		Cordagalma_sp_@1525873
		Rhizophysa_filiformis@3073669
		Hydra_magnipapillata@52244
		Ectopleura_larynx@3556167
	;
END;
BEGIN TREES;
	TRANSLATE
		1	Prayidae_D27SS7@2825365,
		2	Kephyes_ovata@2606431,
		3	Chuniphyes_multidentata@1277217,
		4	Apolemia_sp_@1353964,
		5	Bargmannia_amoena@263997,
		6	Bargmannia_elongata@946788,
		7	Physonect_sp_@2066767,
		8	Stephalia_dilata@2960089,
		9	Frillagalma_vityazi@1155031,
		10	Resomia_ornicephala@3111757,
		11	Lychnagalma_utricularia@2253871,
		12	Nanomia_bijuga@717864,
		13	Cordagalma_sp_@1525873,
		14	Rhizophysa_filiformis@3073669,
		15	Hydra_magnipapillata@52244,
		16	Ectopleura_larynx@3556167
	;
	TREE * UNTITLED = [&R] (((1[&Ev=S,S=58,ND=0]:0.0682841,(2[&Ev=S,S=69,ND=1]:0.0193941,3[&Ev=S,S=70,ND=2]:0.0121378)[&Ev=S,S=60,ND=3]:0.0217782)[&Ev=S,S=36,ND=4]:0.0607598,((4[&Ev=S,S=31,ND=9]:0.11832,(((5[&Ev=S,S=37,ND=10]:0.0144549,6[&Ev=S,S=38,ND=11]:0.0149723)[&Ev=S,S=33,ND=12]:0.0925388,7[&Ev=S,S=61,ND=13]:0.077429)[&Ev=S,S=24,ND=14]:0.0274637,(8[&Ev=S,S=52,ND=15]:0.0761163,((9[&Ev=S,S=53,ND=16]:0.0906068,10[&Ev=S,S=54,ND=17]:1e-06)[&Ev=S,S=45,ND=18]:1e-06,((11[&Ev=S,S=65,ND=19]:0.120851,12[&Ev=S,S=71,ND=20]:0.133939)[&Ev=S,S=56,ND=21]:1e-06,13[&Ev=S,S=64,ND=22]:0.0693814)[&Ev=S,S=46,ND=23]:1e-06)[&Ev=S,S=40,ND=24]:0.0333823)[&Ev=S,S=35,ND=25]:1e-06)[&Ev=D,S=24,ND=26]:0.0431861)[&Ev=S,S=19,ND=27]:1e-06,14[&Ev=S,S=26,ND=28]:0.22283)[&Ev=S,S=17,ND=29]:0.0292362)[&Ev=D,S=17,ND=8]:0.185603,(15[&Ev=S,S=16,ND=5]:0.0621782,16[&Ev=S,S=15,ND=6]:0.332505)[&Ev=S,S=12,ND=7]:0.185603)[&Ev=S,S=9,ND=30];
END;