title: TESS: an R package for efficiently simulating phylogenetic trees and performing Bayesian inference of lineage diversification rates.
abstract: Many fundamental questions in evolutionary biology entail estimating rates of lineage diversification (speciation-extinction) that are modeled using birth-death branching processes. We leverage recent advances in branching-process theory to develop a flexible Bayesian framework for specifying diversification models-where rates are constant, vary continuously, or change episodically through time-and implement numerical methods to estimate parameters of these models from molecular phylogenies, even when species sampling is incomplete. We enable both statistical inference and efficient simulation under these models. We also provide robust methods for comparing the relative and absolute fit of competing branching-process models to a given tree, thereby providing rigorous tests of biological hypotheses regarding patterns and processes of lineage diversification.
  
  
  
  The source code for TESS is freely available at http://cran.r-project.org/web/packages/TESS/ CONTACT: Sebastian.Hoehna@gmail.com.
authors.affiliation: Department of Integrative Biology, Department of Statistics, University of California, Berkeley, CA 94720, USA, Department of Evolution and Ecology, University of California, Davis, CA 95616, USA and Department of Mathematics, Stockholm University, Stockholm, SE-106 91, Sweden.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Höhna
authors.affiliation: Department of Evolution and Ecology, University of California, Davis, CA 95616, USA and.
authors.forename: Michael R
authors.initials: MR
authors.lastname: May
authors.affiliation: Department of Evolution and Ecology, University of California, Davis, CA 95616, USA and.
authors.forename: Brian R
authors.initials: BR
authors.lastname: Moore
mesh_terms: D001499:Bayes Theorem; D005075:Biological Evolution; D003198:Computer Simulation; D010802:Phylogeny; D011381:Programming Languages