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apTreeshape (version 1.4-5)

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.

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Version

Install

install.packages('apTreeshape')

Monthly Downloads

156

Version

1.4-5

License

GPL (>= 2)

Maintainer

Blum Michael

Last Published

November 9th, 2012

Functions in apTreeshape (1.4-5)

all.equal.treeshape

Compare two objects of class treeshape
sackin

Compute the Sackin's index of a tree
apTreeshape-internal

Internal apTreeshape Functions
summary.treeshape

Print a summary of an object of class "treeshape"
shift.test

Testing diversification rate variation in phylogenetic trees
index.test

Perform a test on the Yule or PDA hypothesis based on the Colless or the Sackin statistic
cytochromc

Phylogeny of the cytochrome C family.
as.treeshape

Conversion among tree objects
plot.treeshape

Plot phylogenetic treeshapes.
colless

Compute the Colless' shape statistic on tree data
rhodopsin

Phylogeny of rhodopsin proteins.
rtreeshape

Generate a list of random binary trees according to a given model
smaller.clade.spectrum

Compute the smaller clade spectrum of a tree.
cutreeshape

Cut objects of class "treeshape"
maxlik.betasplit

Maximum likelihood of beta in the Beta-splitting model
cladesize

Compute the number of children of a randomly chosen node
carnivora.treeshape

Phylogeny of carnivores.
subtree.test

Test the Yule or PDA hypothesis
spectrum.treeshape

Compute the spectrum of a tree
treeshape

Builds an object of class treeshape
tipsubtree

Extract a subtree that contains pre-specified tip names or labels
universal.treeshape

Universal phylogenetic tree of life
likelihood.test

Test the Yule model vs PDA (uniform) model.
primates

Phylogeny of the primates.
hivtree.treeshape

Phylogenetic Tree of 193 HIV-1 Sequences
aldous.test

Visualizing balance via scatter diagrams
shape.statistic

Computes the log of the likelihood ratio (yule/pda)
as.phylo.treeshape

Conversion among tree objects