phytools: an R package for phylogenetic comparative biology (and other things)

被引:6943
作者
Revell, Liam J. [1 ]
机构
[1] Univ Massachusetts, Dept Biol, Boston, MA 02125 USA
来源
METHODS IN ECOLOGY AND EVOLUTION | 2012年 / 3卷 / 02期
关键词
blogging; computational biology; evolution; phylogeny; statistics; EVOLUTION; MODELS; SIGNAL; DIVERSIFICATION; INFERENCE; TRAITS; TREES;
D O I
10.1111/j.2041-210X.2011.00169.x
中图分类号
Q14 [生态学(生物生态学)];
学科分类号
071012 ; 0713 ;
摘要
1. Here, I present a new, multifunctional phylogenetics package, phytools, for the R statistical computing environment. 2. The focus of the package is on methods for phylogenetic comparative biology; however, it also includes tools for tree inference, phylogeny input / output, plotting, manipulation and several other tasks. 3. I describe and tabulate the major methods implemented in phytools, and in addition provide some demonstration of its use in the form of two illustrative examples. 4. Finally, I conclude by briefly describing an active web-log that I use to document present and future developments for phytools. I also note other web resources for phylogenetics in the R computational environment.
引用
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页码:217 / 223
页数:7
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