ape

Analyses of Phylogenetics and Evolution

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 DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, 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, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. 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.

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Description file content

Package
ape
Version
5.0
Date
2017-10-04
Title
Analyses of Phylogenetics and Evolution
Depends
R (>= 3.2.0)
Suggests
gee, expm
Imports
nlme, lattice, graphics, methods, stats, tools, utils, parallel, Rcpp (>= 0.12.0)
LinkingTo
Rcpp
ZipData
no
Description
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 DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, 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, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. 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.
License
GPL (>= 2)
URL
NeedsCompilation
yes
Packaged
2017-10-04 16:39:18 UTC; paradis
Author
Emmanuel Paradis [aut, cre, cph], Simon Blomberg [aut, cph], Ben Bolker [aut, cph], Joseph Brown [aut, cph], Julien Claude [aut, cph], Hoa Sien Cuong [aut, cph], Richard Desper [aut, cph], Gilles Didier [aut, cph], Benoit Durand [aut, cph], Julien Dutheil [aut, cph], RJ Ewing [aut, cph], Olivier Gascuel [aut, cph], Christoph Heibl [aut, cph], Anthony Ives [aut, cph], Bradley Jones [aut, cph], Franz Krah [aut, cph], Daniel Lawson [aut, cph], Vincent Lefort [aut, cph], Pierre Legendre [aut, cph], Jim Lemon [aut, cph], Rosemary McCloskey [aut, cph], Johan Nylander [aut, cph], Rainer Opgen-Rhein [aut, cph], Andrei-Alin Popescu [aut, cph], Manuela Royer-Carenzi [aut, cph], Klaus Schliep [aut, cph], Korbinian Strimmer [aut, cph], Damien de Vienne [aut, cph]
Maintainer
Emmanuel Paradis
Repository
CRAN
Date/Publication
2017-10-30 15:36:18 UTC

install.packages('ape')

5.0

a month ago

http://ape-package.ird.fr/

Emmanuel Paradis

GPL (>= 2)

Depends on

R (>= 3.2.0)

Imports

nlme, lattice, graphics, methods, stats, tools, utils, parallel, Rcpp (>= 0.12.0)

Suggests

gee, expm

Discussions