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Analyses of Phylogenetics and Evolution

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 library(help = ape).

More information on ape can be found at http://ape.mpl.ird.fr/.

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References

Paradis, E. (2012) Analysis of Phylogenetics and Evolution with R (Second Edition). New York: Springer.

Paradis, E., Claude, J. and Strimmer, K. (2004) APE: analyses of phylogenetics and evolution in R language. Bioinformatics, 20, 289--290.

Aliases
Documentation reproduced from package ape, version 3.0-2, License: GPL (>= 2)

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