# ape v3.0-11

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## Analyses of Phylogenetics and Evolution

ape provides functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from allelic and nucleotide data, reading and writing nucleotide sequences, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.

## Functions in ape

Name | Description | |

dist.gene | Pairwise Distances from Genetic Data | |

as.bitsplits | Conversion Among Split Classes | |

as.alignment | Conversion Among DNA Sequence Internal Formats | |

all.equal.phylo | Global Comparison of two Phylogenies | |

base.freq | Base frequencies from DNA Sequences | |

MPR | Most Parsimonious Reconstruction | |

ape-internal | Internal Ape Functions | |

clustal | Multiple Sequence Alignment with External Applications | |

c.phylo | Building Lists of Trees | |

collapsed.intervals | Collapsed Coalescent Intervals | |

add.scale.bar | Add a Scale Bar to a Phylogeny Plot | |

corBlomberg | Blomberg et al.'s Correlation Structure | |

branching.times | Branching Times of a Phylogenetic Tree | |

corMartins | Martins's (1997) Correlation Structure | |

consensus | Concensus Trees | |

corPagel | Pagel's ``lambda'' Correlation Structure | |

corGrafen | Grafen's (1989) Correlation Structure | |

compar.lynch | Lynch's Comparative Method | |

is.binary.tree | Test for Binary Tree | |

alex | Alignment Explorer With Multiple Devices | |

multi2di | Collapse and Resolve Multichotomies | |

chronos | Molecular Dating by Penalised Likelihood and Maximum Likelihood | |

data.nex | NEXUS Data Example | |

kronoviz | Plot Multiple Chronograms on the Same Scale | |

as.matching | Conversion Between Phylo and Matching Objects | |

Moran.I | Moran's I Autocorrelation Index | |

ewLasso | Incomplete distances and edge weights of unrooted topology | |

axisPhylo | Axis on Side of Phylogeny | |

mat3 | Three Matrices | |

is.monophyletic | Is Group Monophyletic | |

identify.phylo | Graphical Identification of Nodes and Tips | |

njs | Tree Reconstruction from Incomplete Distances With NJ* or bio-NJ* | |

additive | Incomplete Distance Matrix Filling | |

gammaStat | Gamma-Statistic of Pybus and Harvey | |

mvr | Minimum Variance Reduction | |

print.phylo | Compact Display of a Phylogeny | |

mat5M3ID | Five Trees | |

hivtree | Phylogenetic Tree of 193 HIV-1 Sequences | |

pic | Phylogenetically Independent Contrasts | |

CADM.global | Congruence among distance matrices | |

edges | Draw Additional Edges on a Plotted Tree | |

weight.taxo | Define Similarity Matrix | |

pic.ortho | Phylogenetically Independent Orthonormal Contrasts | |

trex | Tree Explorer With Multiple Devices | |

rTraitCont | Continuous Character Simulation | |

slowinskiguyer.test | Slowinski-Guyer Test of Homogeneous Diversification | |

dbd | Probability Density Under Birth--Death Models | |

dist.topo | Topological Distances Between Two Trees | |

opsin | Gene Tree of 32 opsin Sequences | |

boot.phylo | Tree Bipartition and Bootstrapping Phylogenies | |

cophenetic.phylo | Pairwise Distances from a Phylogenetic Tree | |

is.compatible | Check Compatibility of Splits | |

bird.families | Phylogeny of the Families of Birds From Sibley and Ahlquist | |

collapse.singles | Collapse Single Nodes | |

Initialize.corPhyl | Initialize a `corPhyl' Structure Object | |

compar.gee | Comparative Analysis with GEEs | |

del.gaps | Delete Alignment Gaps in DNA Sequences | |

compar.ou | Ornstein--Uhlenbeck Model for Continuous Characters | |

mcmc.popsize | Reversible Jump MCMC to Infer Demographic History | |

bd.ext | Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates | |

as.phylo.formula | Conversion from Taxonomy Variables to Phylogenetic Trees | |

delta.plot | Delta Plots | |

is.ultrametric | Test if a Tree is Ultrametric | |

compute.brtime | Compute and Set Branching Times | |

corBrownian | Brownian Correlation Structure | |

dist.dna | Pairwise Distances from DNA Sequences | |

read.nexus | Read Tree File in Nexus Format | |

makeNodeLabel | Makes Node Labels | |

rTraitDisc | Discrete Character Simulation | |

diversi.time | Analysis of Diversification with Survival Models | |

varcomp | Compute Variance Component Estimates | |

which.edge | Identifies Edges of a Tree | |

chronopl | Molecular Dating With Penalized Likelihood | |

triangMtd | Tree Reconstruction Based on the Triangles Method | |

compute.brlen | Branch Lengths Computation | |

ape-package | Analyses of Phylogenetics and Evolution | |

mat5Mrand | Five Independent Trees | |

where | Find Patterns in DNA Sequences | |

diversity.contrast.test | Diversity Contrast Test | |

birthdeath | Estimation of Speciation and Extinction Rates With Birth-Death Models | |

matexpo | Matrix Exponential | |

summary.phylo | Print Summary of a Phylogeny | |

howmanytrees | Calculate Numbers of Phylogenetic Trees | |

read.tree | Read Tree File in Parenthetic Format | |

diversi.gof | Tests of Constant Diversification Rates | |

compar.cheverud | Cheverud's Comparative Method | |

evonet | Evolutionary Networks | |

skylineplot | Drawing Skyline Plot Graphs | |

BIONJ | Tree Estimation Based on an Improved Version of the NJ Algorithm | |

rlineage | Tree Simulation Under the Time-Dependent Birth--Death Models | |

subtreeplot | Zoom on a Portion of a Phylogeny by Successive Clicks | |

unique.multiPhylo | Revomes Duplicate Trees | |

ace | Ancestral Character Estimation | |

plot.varcomp | Plot Variance Components | |

read.caic | Read Tree File in CAIC Format | |

write.tree | Write Tree File in Parenthetic Format | |

richness.yule.test | Test of Diversification-Shift With the Yule Process | |

skyline | Skyline Plot Estimate of Effective Population Size | |

plot.correlogram | Plot a Correlogram | |

bd.time | Time-Dependent Birth-Death Models | |

cophyloplot | Plots two phylogenetic trees face to face with links between the tips. | |

multiphylo | Manipulating Lists of Trees | |

rotate | Swapping Sister Clades | |

corClasses | Phylogenetic Correlation Structures | |

mst | Minimum Spanning Tree | |

bind.tree | Binds Trees | |

as.phylo | Conversion Among Tree and Network Objects | |

yule.cov | Fits the Yule Model With Covariates | |

rTraitMult | Multivariate Character Simulation | |

root | Roots Phylogenetic Trees | |

lmorigin | Multiple regression through the origin | |

nj | Neighbor-Joining Tree Estimation | |

ladderize | Ladderize a Tree | |

seg.sites | Find Segregating Sites in DNA Sequences | |

treePop | Tree Popping | |

zoom | Zoom on a Portion of a Phylogeny | |

write.nexus.data | Write Character Data in NEXUS Format | |

yule.time | Fits the Time-Dependent Yule Model | |

mcconwaysims.test | McConway-Sims Test of Homogeneous Diversification | |

mrca | Find Most Recent Common Ancestors Between Pairs | |

SDM | Construction of Consensus Distance Matrix With SDM | |

speciesTree | Species Tree Estimation | |

bird.orders | Phylogeny of the Orders of Birds From Sibley and Ahlquist | |

woodmouse | Cytochrome b Gene Sequences of Woodmice | |

write.nexus | Write Tree File in Nexus Format | |

chiroptera | Bat Phylogeny | |

mantel.test | Mantel Test for Similarity of Two Matrices | |

balance | Balance of a Dichotomous Phylogenetic Tree | |

correlogram.formula | Phylogenetic Correlogram | |

carnivora | Carnivora body sizes and life history traits | |

drop.tip | Remove Tips in a Phylogenetic Tree | |

landplants | Gene Tree of 36 Landplant rbcL Sequences | |

cherry | Number of Cherries and Null Models of Trees | |

phymltest | Fits a Bunch of Models with PhyML | |

plot.phylo | Plot Phylogenies | |

subtrees | All subtrees of a Phylogenetic Tree | |

image.DNAbin | Plot of DNA Sequence Alignement | |

varCompPhylip | Variance Components with Orthonormal Contrasts | |

read.GenBank | Read DNA Sequences from GenBank via Internet | |

reorder.phylo | Internal Reordering of Trees | |

parafit | Test of host-parasite coevolution | |

ltt.plot | Lineages Through Time Plot | |

nodelabels | Labelling the Nodes, Tips, and Edges of a Tree | |

vcv | Phylogenetic Variance-covariance or Correlation Matrix | |

makeLabel | Label Management | |

mixedFontLabel | Mixed Font Labels for Plotting | |

read.dna | Read DNA Sequences in a File | |

node.depth | Depth and Heights of Nodes and Tips | |

read.nexus.data | Read Character Data In NEXUS Format | |

write.dna | Write DNA Sequences in a File | |

rtree | Generates Random Trees | |

FastME | Tree Estimation Based on the Minimum Evolution Algorithm | |

yule | Fits the Yule Model to a Phylogenetic Tree | |

DNAbin | Manipulate DNA Sequences in Bit-Level Format | |

pcoa | Principal Coordinate Analysis | |

chronoMPL | Molecular Dating With Mean Path Lengths | |

stree | Generates Systematic Regular Trees | |

coalescent.intervals | Coalescent Intervals | |

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## Last month downloads

## Details

Date | 2013-10-01 |

ZipData | no |

License | GPL (>= 2) |

URL | http://ape-package.ird.fr/ |

Packaged | 2013-10-01 09:08:43 UTC; paradis |

NeedsCompilation | yes |

Repository | CRAN |

Date/Publication | 2013-10-01 11:19:28 |

depends | base (>= 2.6.0) , R (>= 2.6.0) |

suggests | expm , gee |

imports | graphics , lattice , nlme , stats , tools , utils |

Contributors | Emmanuel Paradis, Ben Bolker, Julien Claude, Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel, Christoph Heibl, Daniel Lawson, Vincent Lefort, Pierre Legendre, Jim Lemon, Johan Nylander, Rainer Opgen-Rhein, Andrei-Alin Popescu, Klaus Schliep, Korbinian Strimmer, Hoa Sien Cuong, Damien de Vienne |

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