pez: phylogenetics for the environmental sciences

William D Pearse; Marc W Cadotte; Jeannine Cavender-Bares; Anthony R Ives; Caroline M Tucker; Steve C Walker; Matthew R Helmus

doi:10.1093/bioinformatics/btv277

pez: phylogenetics for the environmental sciences

Bioinformatics. 2015 Sep 1;31(17):2888-90. doi: 10.1093/bioinformatics/btv277. Epub 2015 May 5.

Authors

William D Pearse¹, Marc W Cadotte², Jeannine Cavender-Bares³, Anthony R Ives⁴, Caroline M Tucker⁵, Steve C Walker⁶, Matthew R Helmus⁷

Affiliations

¹ Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, USA, Department of Biology, McGill University, Montréal, QC, Canada, Département des Sciences Biologiques, Université du Québec à Montréal, Succursale Centre-ville, Montréal, QC, Canada.
² Department of Biological Sciences, University of Toronto Scarborough, Scarborough, ON, Canada.
³ Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, USA.
⁴ Department of Zoology, University of Wisconsin, Madison, WI, USA.
⁵ Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA.
⁶ Department of Mathematics and Statistics, McMaster University, Hamilton, ON, Canada, and.
⁷ Department of Animal Ecology, Vrije Universiteit, Amsterdam, The Netherlands.

PMID: 25948716
DOI: 10.1093/bioinformatics/btv277

Abstract

pez is an R package that permits measurement, modelling and simulation of phylogenetic structure in ecological data. pez contains the first implementation of many methods in R, and aggregates existing data structures and methods into a single, coherent package.

Availability and implementation: pez is released under the GPL v3 open-source license, available on the Internet from CRAN (http://cran.r-project.org). The package is under active development, and the authors welcome contributions (see http://github.com/willpearse/pez).

Contact: will.pearse@gmail.com.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Biodiversity*
Databases, Genetic*
Ecology*
Phenotype
Phylogeny*
Software*