ape swMATH ID: 4569 Software Authors: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong,Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel,Christoph Heibl, Daniel Lawson, Vincent Lefort, PierreLegendre, Jim Lemon, Yvonnick Noel, Johan Nylander, RainerOpgen-Rhein, Andrei-Alin Popescu, Klaus Schliep, KorbinianStrimmer, Damien de Vienne Description: R package ape: Analyses of Phylogenetics and Evolution , ape provides functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from allelic and nucleotide data, reading and writing nucleotide sequences, and several tools such as Mantel’s test, minimum spanning tree, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R. Homepage: http://cran.r-project.org/web/packages/ape/ Source Code: https://github.com/cran/ape Dependencies: R (≥ 2.6.0) Related Software: R; phytools; GEIGER; MrBayes; phangorn; cluster (R); ade4; ggplot2; MASS (R); MAFFT; PHYLIP; BEAST; BEAUti; apTreeshape; ASTRAL-II; PAUP*; RAxML; igraph; dendextend; Picante Cited in: 53 Publications all top 5 Cited by 109 Authors 5 Paradis, Emmanuel 3 Yoshida, Ruriko 2 Bartoszek, Krzysztof 2 Borcard, Daniel 2 Didier, Gilles 2 Fischer, Mareike 2 François, Olivier 2 Gillet, François 2 Jhwueng, Dwueng-Chwuan 2 Legendre, Pierre 2 Lin, Bo 2 Pavoine, Sandrine 2 Royer-Carenzi, Manuela 1 Amiri, Saeid 1 Andersson, Staffan 1 Ané, Cécile 1 Barber, Stuart 1 Baumer, Benjamin S. 1 Bell, Rayna 1 Bivand, Roger S. 1 Blum, Michael G. B. 1 Cappello, Lorenzo 1 Carson, Jake 1 Charleston, Michael A. 1 Chen, Frank Youhua 1 Clarke, Bertrand S. 1 Clarke, Jennifer Lynn 1 Claude, Julien 1 Costa, Carolina L. N. 1 Crawford, Lorin 1 Dehmer, Matthias 1 Devillard, Sébastien 1 Dey, Dipak Kumar 1 Didelot, Xavier 1 Elliot, Michael G. 1 Ferraro, Maria Brigida 1 Ferretti, Luca 1 Freund, Fabian 1 Fukuyama, Julia 1 Ge, Li 1 Gilks, Walter R. 1 Giordani, Paolo E. 1 Glémin, Sylvain 1 Gray, Russell D. 1 Gusnanto, Arief 1 Hansen, Thomas F. 1 Hein, Jotun J. 1 Ho, Lam Si Tung 1 Holsinger, Kent E. 1 Horton, Nicholas J. 1 Ignatieva, Anastasia 1 Jarvis, Peter D. 1 Jenkins, Paul A. 1 Jermiin, Lars S. 1 Jiang, Xun 1 Jombart, Thibaut 1 Kaj, Ingemar 1 Kališnik Verovšek, Sara 1 Kaplan, Daniel T. 1 Keith, Jonathan M. 1 Kersting, Sophie J. 1 Kubatko, Laura Salter 1 Lascoux, Martin 1 Ledda, Alice 1 Liebscher, Volkmar 1 Liu, Jiaguo 1 Mariadassou, Mahendra 1 Maroulas, Vasileios 1 Marquitti, Flavia M. D. 1 Martella, Francesca 1 Martinez de Aguiar, Marcus Aloizio 1 Mioland, Céline 1 Monod, Anthea 1 Mostad, Petter 1 Nicholls, Geoff K. 1 Nooney, Colleen 1 Palacios, Julia A. 1 Patiño-Galindo, Juan Ángel 1 Perez, S. Ivan 1 Pienaar, Jason 1 Podani, János 1 Pontier, Dominique 1 Prunier, Rachel 1 Rahnenführer, Jörg 1 Ramos, Marlon F. 1 Rhodes, John Anthony 1 Richards, Andrew 1 Ricotta, Carlo 1 Robin, Stéphane 1 Roch, Sébastien 1 Schneider, David M. 1 Siri-Jegousse, Arno 1 Sturmfels, Bernd 1 Sumner, Jeremy G. 1 Swenson, Nathan G. 1 Tahir, Daniah 1 Tang, Xiaoxian 1 Vacher, Corinne 1 Warnow, Tandy J. 1 Waxman, David ...and 9 more Authors all top 5 Cited in 25 Serials 12 Journal of Theoretical Biology 5 Use R! 4 Mathematical Biosciences 4 The Annals of Applied Statistics 3 Bulletin of Mathematical Biology 2 Journal of Mathematical Biology 2 SIAM Journal on Discrete Mathematics 2 Computational Statistics and Data Analysis 2 Journal of Computational and Graphical Statistics 1 Physica A 1 Annals of the Institute of Statistical Mathematics 1 Theoretical Population Biology 1 Statistics & Probability Letters 1 Computational Statistics 1 Test 1 Statistical Papers 1 Journal of the Royal Statistical Society. Series B. Statistical Methodology 1 Journal of Biological Systems 1 Statistical Applications in Genetics and Molecular Biology 1 Computational Biology 1 Mathematics 1 SIAM Journal on Applied Algebra and Geometry 1 Chapman & Hall/CRC Texts in Statistical Science Series 1 Methods in Molecular Biology 1 Behaviormetrics: Quantitative Approaches to Human Behavior all top 5 Cited in 15 Fields 39 Biology and other natural sciences (92-XX) 27 Statistics (62-XX) 8 Probability theory and stochastic processes (60-XX) 5 Combinatorics (05-XX) 4 Computer science (68-XX) 3 General and overarching topics; collections (00-XX) 3 Numerical analysis (65-XX) 2 Algebraic geometry (14-XX) 2 Convex and discrete geometry (52-XX) 2 Operations research, mathematical programming (90-XX) 1 Commutative algebra (13-XX) 1 Functions of a complex variable (30-XX) 1 Algebraic topology (55-XX) 1 Statistical mechanics, structure of matter (82-XX) 1 Game theory, economics, finance, and other social and behavioral sciences (91-XX) Citations by Year