Package apTreeshape

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Detailed Description

Title:Analyses of Phylogenetic Treeshape Description:apTreeshape is mainly dedicated to simulation and analysis of phylogenetic tree topologies using statistical indices. It is a companion library of the 'ape' package. It provides additional functions for reading, plotting, manipulating phylogenetic trees. It also offers convenient web-access to public databases, and enables testing null models of macroevolution using corrected test statistics. Trees of class "phylo" (from 'ape' package) can be converted easily.

Author:Nicolas Bortolussi <nicolas.bortolussi@imag.fr>, Eric Durand <eric.durand@imag.fr>, Michael Blum <michael.blum@imag.fr>, Olivier Fran?ois <olivier.francois@imag.fr> Maintainer:Nicolas Bortolussi <nicolas.bortolussi@imag.fr> Version:1.2.0 Built:R 2.2.1; ; 2006-04-05 21:28:46; unix Date:2005-09-01 Depends:R (>= 2.0.0) License:GPL version 2 or later Packaged:Fri Feb 10 12:00:52 2006; edurand Suggests:ape, quantreg

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cladesize
Compute the number of children of a randomly chosen node

Last ouput from cladesize(). For all plots see PDF file.

PDF output with all plots
Example code and log output is in the "Files" section, please see: apTreeshape/cladesize/example.log

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colless
Compute the Colless' shape statistic on tree data

Last ouput from colless(). For all plots see PDF file.

PDF output with all plots
Example code and log output is in the "Files" section, please see: apTreeshape/colless/example.log

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cytochromc
Phylogenetic trees from the Pandit database

Last ouput from cytochromc(). For all plots see PDF file.

PDF output with all plots
Example code and log output is in the "Files" section, please see: apTreeshape/cytochromc/example.log

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hivtree.treeshape
Phylogenetic Tree of 193 HIV-1 Sequences

Last ouput from hivtree.treeshape(). For all plots see PDF file.

PDF output with all plots
Example code and log output is in the "Files" section, please see: apTreeshape/hivtree.treeshape/example.log

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primates
Phylogenetic trees from the TreeBASE database

Last ouput from primates(). For all plots see PDF file.

PDF output with all plots
Example code and log output is in the "Files" section, please see: apTreeshape/primates/example.log

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rtreeshape
Generate a list of random binary trees according to a given model

Last ouput from rtreeshape(). For all plots see PDF file.

PDF output with all plots
Example code and log output is in the "Files" section, please see: apTreeshape/rtreeshape/example.log

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sackin
Compute the Sackin's index of a tree

Last ouput from sackin(). For all plots see PDF file.

PDF output with all plots
Example code and log output is in the "Files" section, please see: apTreeshape/sackin/example.log

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universal.treeshape
Universal phylogenetic tree of life

Last ouput from universal.treeshape(). For all plots see PDF file.

PDF output with all plots
Example code and log output is in the "Files" section, please see: apTreeshape/universal.treeshape/example.log

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