iteRates: An R Package for Implementing a Parametric Rate Comparison on Phylogenetic Trees | Zendy

James A. Fordyce | Zendy; Premal Shah | Zendy; Benjamin M. Fitzpatrick | Zendy

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iteRates: An R Package for Implementing a Parametric Rate Comparison on Phylogenetic Trees

Author(s) -

James A. Fordyce,

Premal Shah,

Benjamin M. Fitzpatrick

Publication year - 2014

Publication title -

evolutionary bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 0.502

H-Index - 32

ISSN - 1176-9343

DOI - 10.4137/ebo.s16487

Subject(s) - phylogenetic tree , iterated function , r package , clade , tree (set theory) , diversification (marketing strategy) , computer science , parametric statistics , phylogenetics , statistics , evolutionary biology , biology , mathematics , combinatorics , mathematical analysis , biochemistry , marketing , gene , business

Patterns of diversification rate variation detected in phylogenetic hypotheses are frequently used to infer historical, ecological, and evolutionary processes. The parametric rate comparison (PRC) is a method for detecting rate variation in trees that models branch lengths as random variables drawn from familiar statistical distributions. iteRates is a library of functions for the R statistical computing environment for implementing PRC on phylogenetic trees. Here, we describe some of the functions in iteRates for subtree identification, tree manipulation, applying the PRC and K-clades PRC analyses, and conducting a whole-tree randomization test.

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