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Article: Treeio: An R Package for Phylogenetic Tree Input and Output with Richly Annotated and Associated Data

TitleTreeio: An R Package for Phylogenetic Tree Input and Output with Richly Annotated and Associated Data
Authors
Editors
Editor(s):Kumar, S
Keywordsdata integration
phylogeny
ggtree
bioconductor
Issue Date2020
PublisherOxford University Press. The Journal's web site is located at http://mbe.oxfordjournals.org/
Citation
Molecular Biology and Evolution, 2020, v. 37 n. 2, p. 599-603 How to Cite?
AbstractPhylogenetic trees and data are often stored in incompatible and inconsistent formats. The outputs of software tools that contain trees with analysis findings are often not compatible with each other, making it hard to integrate the results of different analyses in a comparative study. The treeio package is designed to connect phylogenetic tree input and output. It supports extracting phylogenetic trees as well as the outputs of commonly used analytical software. It can link external data to phylogenies and merge tree data obtained from different sources, enabling analyses of phylogeny-associated data from different disciplines in an evolutionary context. Treeio also supports export of a phylogenetic tree with heterogeneous-associated data to a single tree file, including BEAST compatible NEXUS and jtree formats; these facilitate data sharing as well as file format conversion for downstream analysis. The treeio package is designed to work with the tidytree and ggtree packages. Tree data can be processed using the tidy interface with tidytree and visualized by ggtree. The treeio package is released within the Bioconductor and rOpenSci projects. It is available at https://www.bioconductor.org/packages/treeio/.
Persistent Identifierhttp://hdl.handle.net/10722/287240
ISSN
2019 Impact Factor: 11.062
2015 SCImago Journal Rankings: 8.168
PubMed Central ID

 

DC FieldValueLanguage
dc.contributor.authorWang, LG-
dc.contributor.authorLam, TTY-
dc.contributor.authorXu, S-
dc.contributor.authorDai, Z-
dc.contributor.authorZhou, L-
dc.contributor.authorFeng, T-
dc.contributor.authorGuo, P-
dc.contributor.authorDunn, CW-
dc.contributor.authorJones, BR-
dc.contributor.authorBradley, T-
dc.contributor.authorZhu, H-
dc.contributor.authorGuan, Y-
dc.contributor.authorJiang, Y-
dc.contributor.authorYu, G-
dc.contributor.editorKumar, S-
dc.date.accessioned2020-09-22T02:57:58Z-
dc.date.available2020-09-22T02:57:58Z-
dc.date.issued2020-
dc.identifier.citationMolecular Biology and Evolution, 2020, v. 37 n. 2, p. 599-603-
dc.identifier.issn0737-4038-
dc.identifier.urihttp://hdl.handle.net/10722/287240-
dc.description.abstractPhylogenetic trees and data are often stored in incompatible and inconsistent formats. The outputs of software tools that contain trees with analysis findings are often not compatible with each other, making it hard to integrate the results of different analyses in a comparative study. The treeio package is designed to connect phylogenetic tree input and output. It supports extracting phylogenetic trees as well as the outputs of commonly used analytical software. It can link external data to phylogenies and merge tree data obtained from different sources, enabling analyses of phylogeny-associated data from different disciplines in an evolutionary context. Treeio also supports export of a phylogenetic tree with heterogeneous-associated data to a single tree file, including BEAST compatible NEXUS and jtree formats; these facilitate data sharing as well as file format conversion for downstream analysis. The treeio package is designed to work with the tidytree and ggtree packages. Tree data can be processed using the tidy interface with tidytree and visualized by ggtree. The treeio package is released within the Bioconductor and rOpenSci projects. It is available at https://www.bioconductor.org/packages/treeio/.-
dc.languageeng-
dc.publisherOxford University Press. The Journal's web site is located at http://mbe.oxfordjournals.org/-
dc.relation.ispartofMolecular Biology and Evolution-
dc.rightsPre-print: Journal Title] ©: [year] [owner as specified on the article] Published by Oxford University Press [on behalf of xxxxxx]. All rights reserved. Pre-print (Once an article is published, preprint notice should be amended to): This is an electronic version of an article published in [include the complete citation information for the final version of the Article as published in the print edition of the Journal.] Post-print: This is a pre-copy-editing, author-produced PDF of an article accepted for publication in [insert journal title] following peer review. The definitive publisher-authenticated version [insert complete citation information here] is available online at: xxxxxxx [insert URL that the author will receive upon publication here].-
dc.subjectdata integration-
dc.subjectphylogeny-
dc.subjectggtree-
dc.subjectbioconductor-
dc.titleTreeio: An R Package for Phylogenetic Tree Input and Output with Richly Annotated and Associated Data-
dc.typeArticle-
dc.identifier.emailLam, TTY: ttylam@hku.hk-
dc.identifier.emailZhu, H: zhuhch@hku.hk-
dc.identifier.emailGuan, Y: yguan@hkucc.hku.hk-
dc.identifier.authorityLam, TTY=rp01733-
dc.identifier.authorityZhu, H=rp01535-
dc.identifier.authorityGuan, Y=rp00397-
dc.description.naturelink_to_OA_fulltext-
dc.identifier.doi10.1093/molbev/msz240-
dc.identifier.pmid31633786-
dc.identifier.pmcidPMC6993851-
dc.identifier.scopuseid_2-s2.0-85078868754-
dc.identifier.hkuros314563-
dc.identifier.volume37-
dc.identifier.issue2-
dc.identifier.spage599-
dc.identifier.epage603-
dc.publisher.placeUnited States-

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