Rphylip: an R interface for PHYLIP

A Comparative Method for Both Discrete and Continuous Characters Using the Threshold Model

(2012) Joseph Felsenstein   AMERICAN NATURALIST

MODELING STABILIZING SELECTION: EXPANDING THE ORNSTEIN-UHLENBECK MODEL OF ADAPTIVE EVOLUTION

(2012) Jeremy M. Beaulieu et al.   EVOLUTION

Diversitree: comparative phylogenetic analyses of diversification in R

(2012) Richard G. FitzJohn   Methods in Ecology and Evolution

paleotree: an R package for paleontological and phylogenetic analyses of evolution

(2012) David W. Bapst   Methods in Ecology and Evolution

Seeing the Forest for the Trees: The Limitations of Phylogenies in Comparative Biology

(2011) Jonathan B. Losos   AMERICAN NATURALIST

How do plants balance multiple mutualists? Correlations among traits for attracting protective bodyguards and pollinators in cotton (Gossypium)

(2011) Scott A. Chamberlain et al.   EVOLUTIONARY ECOLOGY

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

(2011) Liam J. Revell   Methods in Ecology and Evolution

Picante: R tools for integrating phylogenies and ecology

(2010) S. W. Kembel et al.   BIOINFORMATICS

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Comparative Methods with Sampling Error and Within‐Species Variation: Contrasts Revisited and Revised

(2008) Joseph Felsenstein   AMERICAN NATURALIST