Package: ape
Version: 1.10
Date: 2007-05-01
Title: Analyses of Phylogenetics and Evolution
Author: Ben Bolker, Julien Claude, Beno�t Durand,
Julien Dutheil, Gangolf Jobb, Jim Lemon, Yvonnick No�l,
Johan Nylander, Rainer Opgen-Rhein, Emmanuel Paradis,
Korbinian Strimmer
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@mpl.ird.fr>
Depends: R (>= 2.0.0)
Suggests: 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, the population
parameter theta based on various approaches, nucleotide diversity,
generalized skyline plots, estimation of absolute evolutionary rates
and clock-like trees using non-parametric rate smoothing and penalized
likelihood, classifying genes in trees using the Klastorin-Misawa-Tajima
approach. Phylogeny estimation can be done with the NJ and ML methods.
License: GPL version 2 or newer
URL: http://pbil.univ-lyon1.fr/R/ape/
Packaged: Tue May  1 11:47:33 2007; paradis

Packaged: Mon May 24 00:31:49 2004; PARADYS

Packaged: Fri Aug  6 15:07:25 2004; PARADYS

Packaged: Fri Aug 20 21:59:04 2004; PARADYS

Packaged: Thu Sep 16 21:39:46 2004; PARADYS

Packaged: Fri Sep 24 09:49:28 2004; PARADYS

Packaged: Wed Nov 10 17:17:55 2004; PARADYS

Packaged: Wed Nov  3 19:25:39 2004; PARADYS

Packaged: Thu Dec 23 16:08:33 2004; PARADYS

and clock-like trees using non-parametric rate smoothing, conversion
of APE trees to and from hclust objects and for classifying genes in
trees using the Klastorin-Misawa-Tajima approach.
Packaged: Fri Apr 15 20:45:11 2005; root

Packaged: Fri Jun  3 10:33:04 2005; paradis

Packaged: Mon Sep 19 10:56:36 2005; paradis

Packaged: Fri Feb 17 17:30:18 2006; hornik

trees using the Klastorin-Misawa-Tajima approach. Phylogeny estimation
Packaged: Fri Mar 24 03:42:08 2006; paradis