| SiPhyNetwork | A Phylogenetic Simulator for Reticulate Evolution Joshua Justison , Claudia Solis-Lemus , Tracy A. Heath , Klaus Schliep , Emmanuel Paradis , Daniel Lawson |
| adegenet | Exploratory Analysis of Genetic and Genomic Data Thibaut Jombart , Zhian N. Kamvar , Caitlin Collins , Roman Lustrik , Marie-Pauline Beugin , Brian J. Knaus , Peter Solymos , Vladimir Mikryukov , Klaus Schliep , Tiago Maié , Libor Morkovsky , Ismail Ahmed , Anne Cori , Federico Calboli , RJ Ewing , Frédéric Michaud , Rebecca DeCamp , Alexandre Courtiol , Lindsay V. Clark , Pavel Dimens |
| 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 |
| apex | Phylogenetic Methods for Multiple Gene Data Klaus Schliep , Thibaut Jombart , Zhian Namir Kamvar , Eric Archer , Rebecca Harris |
| canaper | Categorical Analysis of Neo- And Paleo-Endemism Joel H. Nitta , Shawn W. Laffan , Brent D. Mishler , Wataru Iwasaki , Klaus Schliep |
| datelife | Scientific Data on Time of Lineage Divergence for Your Taxa Brian O'Meara , Jonathan Eastman , Tracy Heath , April Wright , Klaus Schliep , Scott Chamberlain , Peter Midford , Luke Harmon , Joseph Brown , Matt Pennell , Mike Alfaro , Luna L. Sanchez Reyes , Emily Jane McTavish |
| kknn | Weighted k-Nearest Neighbors Klaus Schliep , Klaus Hechenbichler , Antoine Lizee |
| 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 |
| phyloregion | Biogeographic Regionalization and Macroecology Barnabas H. Daru , Piyal Karunarathne , Klaus Schliep , Xiaobei Zhao , Albin Sandelin , Luciano Pataro |
| rCNV | Detect Copy Number Variants from SNPs Data Piyal Karunarathne , Qiujie Zhou , Klaus Schliep , Pascal Milesi |
| rWind | Download, Edit and Include Wind and Sea Currents Data in Ecological and Evolutionary Analysis Javier Fernández-López , Klaus Schliep , Yurena Arjona |
| rwty | R We There Yet? Visualizing MCMC Convergence in Phylogenetics Dan Warren , Anthony Geneva , Rob Lanfear , Luke Harmon , April Wright , Diego Mallo , Klaus Schliep |
| 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 |