IteRates: An R Package for Implementing a Parametric Rate Comparison on Phylogenetic Trees. (January 2014)

• Record Type: Journal Article
• Authors: Fordyce, James A.; Shah, Premal; Fitzpatrick, Benjamin M.
• Is Part Of: Evolutionary bioinformatics online. Volume 10(2014)
• Publication Date: 2014-01
• Subjects: chronogram -- diversification-rate -- phylogeny -- rate-variation; Bioinformatics -- Periodicals; Evolutionary computation -- Periodicals; Genetic programming (Computer science) -- Periodicals; Computational Biology; Evolution, Molecular; Bioinformatics; Electronic journals; Periodicals; Fulltext; Internet Resources; Periodicals; Periodicals; 576.8
• DOI: 10.4137/EBO.S16487
• Languages: English
• ISSNs: 1176-9343

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.