| SiPhyNetwork | A Phylogenetic Simulator for Reticulate Evolution Joshua Justison , Claudia Solis-Lemus , Tracy A. Heath , Klaus Schliep , Emmanuel Paradis , Daniel Lawson |
| TreeTools | Create, Modify and Analyse Phylogenetic Trees Martin R. Smith , Emmanuel Paradis |
| ape | Analyses of Phylogenetics and Evolution Emmanuel Paradis , Simon Blomberg , Ben Bolker , Joseph Brown , Santiago Claramunt , Julien Claude , Hoa Sien Cuong , Richard Desper , Gilles Didier , Benoit Durand , Julien Dutheil , RJ Ewing , Olivier Gascuel , Thomas Guillerme , Christoph Heibl , Anthony Ives , Bradley Jones , Franz Krah , Daniel Lawson , Vincent Lefort , Pierre Legendre , Jim Lemon , Guillaume Louvel , Eric Marcon , Rosemary McCloskey , Johan Nylander , Rainer Opgen-Rhein , Andrei-Alin Popescu , Manuela Royer-Carenzi , Klaus Schliep , Korbinian Strimmer , Damien de Vienne |
| coalescentMCMC | MCMC Algorithms for the Coalescent Emmanuel Paradis |
| motmot | Models of Trait Macroevolution on Trees Mark Puttick , Gavin Thomas , Rob Freckleton , Magnus Clarke , Travis Ingram , David Orme , Emmanuel Paradis |
| mvMORPH | Multivariate Comparative Tools for Fitting Evolutionary Models to Morphometric Data Julien Clavel , Aaron King , Emmanuel Paradis |
| pegas | Population and Evolutionary Genetics Analysis System Emmanuel Paradis , Thibaut Jombart , Zhian N. Kamvar , Brian Knaus , Klaus Schliep , Alastair Potts , David Winter |
| phangorn | Phylogenetic Reconstruction and Analysis Klaus Schliep , Emmanuel Paradis , Leonardo de Oliveira Martins , Alastair Potts , Iris Bardel-Kahr , Tim W. White , Cyrill Stachniss , Michelle Kendall , Keren Halabi , Richel Bilderbeek , Kristin Winchell , Liam Revell , Mike Gilchrist , Jeremy Beaulieu , Brian O'Meara , Long Qu , Joseph Brown , Santiago Claramunt |
| shipunov | Miscellaneous Functions from Alexey Shipunov Alexey Shipunov , Paul Murrell , Marcello D'Orazio , Stephen Turner , Eugeny Altshuler , Rol , Rau , Marcus W Beck , Sebastian Gibb , Weiliang Qiu , Emmanuel Paradis , Roger Koenker , R Core Team |
| tigers | Integration of Geography, Environment, and Remote Sensing Emmanuel Paradis |
| treeducken | Nested Phylogenetic Tree Simulator Wade Dismukes , Tracy A. Heath , Josh Justison , Damien de Vienne , Liam Revell , Emmanuel Paradis , Klaus Schliep , Ben Bolker , Luke J. Harmon , Joseph W. Brown |