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treeman: an R package for efficient and intuitive manipulation of phylogenetic trees

Bennett, DJ; Sutton, MD; Turvey, ST; (2017) treeman: an R package for efficient and intuitive manipulation of phylogenetic trees. BMC Research Notes , 10 , Article 30. 10.1186/s13104-016-2340-8. Green open access

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Abstract

BACKGROUND: Phylogenetic trees are hierarchical structures used for representing the inter-relationships between biological entities. They are the most common tool for representing evolution and are essential to a range of fields across the life sciences. The manipulation of phylogenetic trees—in terms of adding or removing tips—is often performed by researchers not just for reasons of management but also for performing simulations in order to understand the processes of evolution. Despite this, the most common programming language among biologists, R, has few class structures well suited to these tasks. RESULTS: We present an R package that contains a new class, called TreeMan, for representing the phylogenetic tree. This class has a list structure allowing phylogenetic trees to be manipulated more efficiently. Computational running times are reduced because of the ready ability to vectorise and parallelise methods. Development is also improved due to fewer lines of code being required for performing manipulation processes. CONCLUSIONS: We present three use cases—pinning missing taxa to a supertree, simulating evolution with a tree-growth model and detecting significant phylogenetic turnover—that demonstrate the new package’s speed and simplicity.

Type: Article
Title: treeman: an R package for efficient and intuitive manipulation of phylogenetic trees
Open access status: An open access version is available from UCL Discovery
DOI: 10.1186/s13104-016-2340-8
Publisher version: http://doi.org/10.1186/s13104-016-2340-8
Language: English
Additional information: © The Author(s) 2017. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Keywords: Phylogenetic trees; Evolution; Tree simulation; R; Statistical computing
UCL classification: UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
URI: http://discovery.ucl.ac.uk/id/eprint/1535186
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