apTreeshape: Analyses of Phylogenetic Treeshape

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.

Install the latest version of this package by entering the following in R:
install.packages("apTreeshape")
AuthorNicolas Bortolussi, Eric Durand, Michael Blum <michael.blum@imag.fr>, Olivier Francois <olivier.francois@imag.fr>
Date of publication2012-11-09 07:03:26
MaintainerMichael Blum <michael.blum@imag.fr>
LicenseGPL (>= 2)
Version1.4-5

View on CRAN

Man pages

aldous.test: Visualizing balance via scatter diagrams

all.equal.treeshape: Compare two objects of class treeshape

apTreeshape-internal: Internal apTreeshape Functions

as.phylo.treeshape: Conversion among tree objects

as.treeshape: Conversion among tree objects

carnivora.treeshape: Phylogeny of carnivores.

cladesize: Compute the number of children of a randomly chosen node

colless: Compute the Colless' shape statistic on tree data

cutreeshape: Cut objects of class "treeshape"

cytochromc: Phylogeny of the cytochrome C family.

hivtree.treeshape: Phylogenetic Tree of 193 HIV-1 Sequences

index.test: Perform a test on the Yule or PDA hypothesis based on the...

likelihood.test: Test the Yule model vs PDA (uniform) model.

maxlik.betasplit: Maximum likelihood of beta in the Beta-splitting model

plot.treeshape: Plot phylogenetic treeshapes.

primates: Phylogeny of the primates.

rhodopsin: Phylogeny of rhodopsin proteins.

rtreeshape: Generate a list of random binary trees according to a given...

sackin: Compute the Sackin's index of a tree

shape.statistic: Computes the log of the likelihood ratio (yule/pda)

shift.test: Testing diversification rate variation in phylogenetic trees

smaller.clade.spectrum: Compute the smaller clade spectrum of a tree.

spectrum.treeshape: Compute the spectrum of a tree

subtree.test: Test the Yule or PDA hypothesis

summary.treeshape: Print a summary of an object of class "treeshape"

tipsubtree: Extract a subtree that contains pre-specified tip names or...

treeshape: Builds an object of class treeshape

universal.treeshape: Universal phylogenetic tree of life

Functions

aldous.test Man page
all.equal.treeshape Man page
ancestor Man page
as.phylo.treeshape Man page
as.treeshape Man page
as.treeshape.phylo Man page
as.treeshape.treebalance Man page
carnivora.treeshape Man page
cladesize Man page
colless Man page
colless.test Man page
cutreeshape Man page
cytochromc Man page
Delta Man page
hivtree.treeshape Man page
is.binary.phylo Man page
likelihood.test Man page
logratio Man page
maxlik.betasplit Man page
pandit Man page
plot.treeshape Man page
primates Man page
raldous Man page
rbiased Man page
read.tree2 Man page
rhodopsin Man page
rpda Man page
rtreeshape Man page
ryule Man page
sackin Man page
sackin.test Man page
shape.statistic Man page
shift.test Man page
smaller.clade.spectrum Man page
smaller.clade.spectrum2 Man page
spectrum.treeshape Man page
subtree.test Man page
summary.treeshape Man page
tipsubtree Man page
treebalance Man page
treebase Man page
treeshape Man page
universal.treeshape Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.