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 <michael.blum@imag.fr>, Olivier Francois <olivier.francois@imag.fr> |

Date of publication | 2012-11-09 07:03:26 |

Maintainer | Michael Blum <michael.blum@imag.fr> |

License | GPL (>= 2) |

Version | 1.4-5 |

**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

apTreeshape

apTreeshape/MD5

apTreeshape/R

apTreeshape/R/treeshape.R
apTreeshape/R/treebalance.R
apTreeshape/R/tipsubtree.R
apTreeshape/R/summary.treeshape.R
apTreeshape/R/subtree.test.R
apTreeshape/R/spectrum.treeshape.R
apTreeshape/R/smaller.clade.spectrum2.R
apTreeshape/R/smaller.clade.spectrum.R
apTreeshape/R/shift.test.R
apTreeshape/R/shape.statistic.R
apTreeshape/R/sackin.test.R
apTreeshape/R/sackin.R
apTreeshape/R/ryule.R
apTreeshape/R/rtreeshape.R

apTreeshape/R/rpda.R
apTreeshape/R/read.tree2.R
apTreeshape/R/rbiased.R
apTreeshape/R/raldous.R
apTreeshape/R/plot.treeshape.R
apTreeshape/R/maxlik.betasplit.R
apTreeshape/R/logratio.R
apTreeshape/R/likelihood.test.R
apTreeshape/R/is.binary.phylo.R
apTreeshape/R/Delta.R
apTreeshape/R/cutreeshape.R
apTreeshape/R/colless.test.R
apTreeshape/R/colless.R
apTreeshape/R/cladesize.R
apTreeshape/R/as.treeshape.treebalance.R
apTreeshape/R/as.treeshape.R
apTreeshape/R/as.treeshape.phylo.R
apTreeshape/R/as.phylo.treeshape.R
apTreeshape/R/ancestor.R
apTreeshape/R/all.equal.treeshape.R
apTreeshape/R/aldous.test.R
apTreeshape/NAMESPACE

apTreeshape/man

apTreeshape/man/universal.treeshape.Rd
apTreeshape/man/treeshape.Rd
apTreeshape/man/tipsubtree.Rd
apTreeshape/man/summary.treeshape.Rd
apTreeshape/man/subtree.test.Rd
apTreeshape/man/spectrum.treeshape.Rd
apTreeshape/man/smaller.clade.spectrum.Rd
apTreeshape/man/shift.test.Rd
apTreeshape/man/shape.statistic.Rd
apTreeshape/man/sackin.Rd
apTreeshape/man/rtreeshape.Rd
apTreeshape/man/rhodopsin.Rd
apTreeshape/man/primates.Rd
apTreeshape/man/plot.treeshape.Rd
apTreeshape/man/maxlik.betasplit.Rd
apTreeshape/man/likelihood.test.Rd
apTreeshape/man/index.test.Rd
apTreeshape/man/hivtree.treeshape.Rd
apTreeshape/man/cytochromc.Rd
apTreeshape/man/cutreeshape.Rd
apTreeshape/man/colless.Rd
apTreeshape/man/cladesize.Rd
apTreeshape/man/carnivora.treeshape.Rd
apTreeshape/man/as.treeshape.Rd
apTreeshape/man/as.phylo.treeshape.Rd
apTreeshape/man/apTreeshape-internal.Rd
apTreeshape/man/all.equal.treeshape.Rd
apTreeshape/man/aldous.test.Rd
apTreeshape/DESCRIPTION

apTreeshape/demo

apTreeshape/demo/apTreeshape.R

apTreeshape/demo/00Index

apTreeshape/data

apTreeshape/data/universal.treeshape.rda

apTreeshape/data/rhodopsin.rda

apTreeshape/data/primates.rda

apTreeshape/data/hivtree.treeshape.rda

apTreeshape/data/cytochromc.rda

apTreeshape/data/carnivora.treeshape.rda

apTreeshape/CHANGES

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