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rotl : an R package to interact with the Open Tree of Life data
Author(s) -
Michonneau François,
Brown Joseph W.,
Winter David J.
Publication year - 2016
Publication title -
methods in ecology and evolution
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.425
H-Index - 105
ISSN - 2041-210X
DOI - 10.1111/2041-210x.12593
Subject(s) - computer science , tree (set theory) , download , r package , phylogenetic tree , set (abstract data type) , tree of life (biology) , reuse , information retrieval , data science , data set , data mining , world wide web , biology , ecology , artificial intelligence , mathematical analysis , biochemistry , mathematics , gene , programming language , computational science
SummaryWhile phylogenies have been getting easier to build, it has been difficult to reuse, combine and synthesize the information they provide because published trees are often only available as image files, and taxonomic information is not standardized across studies. The Open Tree of Life ( OTL ) project addresses these issues by providing a digital tree that encompasses all organisms, built by combining taxonomic information and published phylogenies. The project also provides tools and services to query and download parts of this synthetic tree, as well as the source data used to build it. Here, we present rotl , an R package to search and download data from the Open Tree of Life directly in R.rotl uses common data structures allowing researchers to take advantage of the rich set of tools and methods that are available in R to manipulate, analyse and visualize phylogenies. Here, and in the vignettes accompanying the package, we demonstrate how rotl can be used with other R packages to analyse biodiversity data. As phylogenies are being used in a growing number of applications, rotl facilitates access to phylogenetic data and allows their integration with statistical methods and data sources available in R.