ape-package

ape provides functions for reading and manipulating phylogenetic
 trees and DNA sequences, computing DNA distances, estimating trees
 with distance-based methods, and a range of methods for comparative
 analyses and analysis of diversification. Functionalities are also
 provided for programming new phylogenetic methods. The complete list of functions can be displayed with
 <code>library(help = ape)</code>. More information on ape can be found at <a href="http://ape-package.ird.fr/">http://ape-package.ird.fr/</a>.

package

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, MAFFT) whose results are returned into R.

Emmanuel Paradis

Analyses of Phylogenetics and Evolution

ape-package function

ape provides functions for reading and manipulating phylogenetic
 trees and DNA sequences, computing DNA distances, estimating trees
 with distance-based methods, and a range of methods for comparative
 analyses and analysis of diversification. Functionalities are also
 provided for programming new phylogenetic methods.

 The complete list of functions can be displayed with
 <code>library(help = ape)</code>.

 More information on ape can be found at <a href = 'http://ape-package.ird.fr/'>http://ape-package.ird.fr/</a>.

ape-package: Analyses of Phylogenetics and Evolution

Description

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