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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

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