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, Eric Durand, Michael Blum <firstname.lastname@example.org>, Olivier Francois <email@example.com>|
|Date of publication||2012-11-09 07:03:26|
|Maintainer||Michael Blum <firstname.lastname@example.org>|
|License||GPL (>= 2)|
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