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

Source Publication

Evolutionary Bioinformatics

Authors

James A. Fordyce, University of Tennessee - KnoxvilleFollow
Premal Shah, University of Tennessee - Knoxville
Benjamin M Fitzpatrick, University of Tennessee - KnoxvilleFollow

Document Type

Article

Publication Date

6-2014

DOI

10.4137/EBO.S16487

Abstract

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.

Comments

This article was published openly thanks to the University of Tennessee Open Publishing Support Fund.

Licensed under a Creative Commons Attribution-Noncommercial 3.0 License.

Recommended Citation

Fordyce, J. A.; Shah, P. & Fitzpatrick, B. M. iteRates: An R Package for Implementing a Parametric Rate Comparison on Phylogenetic Trees Evolutionary Bioinformatics, 2014, 10, 127-130. doi: 10.4137/EBO.S16487

Submission Type

Publisher's Version