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Journal article
Treeio: An R Package for Phylogenetic Tree Input and Output with Richly Annotated and Associated Data
MOLECULAR BIOLOGY AND EVOLUTION, v 37(2), pp 599-603
Feb 2020
PMID: 31633786
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
Phylogenetic 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.
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Details
- Title
- Treeio: An R Package for Phylogenetic Tree Input and Output with Richly Annotated and Associated Data
- Publication Details
- MOLECULAR BIOLOGY AND EVOLUTION, v 37(2), pp 599-603
- Publisher
- OXFORD UNIV PRESS; OXFORD
- Number of pages
- 0
- Grant note
- We would like to thank Drs Scott Chamberlain, Francois Michonneau and Josef Uyeda (rOpenSci) and Prof. Martin Morgan (Bioconductor) for providing thorough code review, and the anonymous reviewers for comments on the article. This work was supported by research grants from National Key Plan for Scientific Research and Development of China (2016YFD0500302; 2017YFE0190800), Shenzhen Peacock Plan (KQTD201203), National Institutes of Health (HHSN272201400006C), NSFC-Guangdong Joint Foundation of China (U1601225), Open Project of Guangdong Provincial Key Laboratory of Proteomics (20191001A), and Startup fund from Southern Medical University (G618289088).
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Drexel University
- Web of Science ID
- WOS:000518533800024
- Scopus ID
- 2-s2.0-85078868754
- Other Identifier
- 991021860771204721
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- Collaboration types
- Domestic collaboration
- International collaboration
- Web of Science research areas
- Biochemistry & Molecular Biology
- Evolutionary Biology
- Genetics & Heredity