Package: ape
Version: 3.0-1
Date: 2012-02-17
Title: Analyses of Phylogenetics and Evolution
Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong,
Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel,
Christoph Heibl, Daniel Lawson, Vincent Lefort, Pierre
Legendre, Jim Lemon, Yvonnick Noel, Johan Nylander, Rainer
Opgen-Rhein, Andrei-Alin Popescu, Klaus Schliep, Korbinian
Strimmer, Damien de Vienne
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
Depends: R (>= 2.6.0)
Suggests: gee
Imports: gee, nlme, lattice
ZipData: no
Description: ape provides functions for reading, writing, plotting, and
manipulating phylogenetic trees, analyses of comparative data
in a phylogenetic framework, analyses of diversification and
macroevolution, computing distances from allelic and nucleotide
data, reading nucleotide sequences, and several tools such as
Mantel's test, computation of minimum spanning tree,
generalized skyline plots, estimation of absolute evolutionary
rates and clock-like trees using mean path lengths,
non-parametric rate smoothing 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).
License: GPL (>= 2)
URL: http://ape.mpl.ird.fr/
Packaged: 2012-02-20 07:59:43 UTC; paradis
Repository: CRAN
Date/Publication: 2012-02-20 09:24:49

Authors@R: c(person("Emmanuel", "Paradis", role = c("aut", "cre", "cph"), email = "Emmanuel.Paradis@ird.fr"),
person("Julien", "Claude", role = "aut"),
person("Hoa Sien", "Cuong", role = "aut"),
person("Richard", "Desper", role = "aut"),
person("Benoit", "Durand", role = "aut"),
person("Julien", "Dutheil", role = "aut"),
person("Olivier", "Gascuel", role = "aut"),
person("Christoph", "Heibl", role = "aut"),
person("Daniel", "Lawson", role = "aut"),
person("Vincent", "Lefort", role = "aut"),
person("Pierre", "Legendre", role = "aut"),
person("Johan", "Nylander", role = "aut"),
person("Rainer", "Opgen-Rhein", role = "aut"),
person("Andrei-Alin", "Popescu", role = "aut"),
person("Klaus", "Schliep", role = "aut"),
person("Korbinian", "Strimmer", role = "aut"),
person("Damien", "de Vienne", role = "aut"))
Imports: nlme, lattice, graphics, stats, tools, utils
Description: 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, 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.
Author: Emmanuel Paradis [aut, cre, cph],