# ape v3.1-4

Monthly downloads

## 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 | |

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

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

coalescent.intervals | Coalescent Intervals | |

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

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

ape-package | Analyses of Phylogenetics and Evolution | |

SDM | Construction of Consensus Distance Matrix With SDM | |

collapse.singles | Collapse Single Nodes | |

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

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

alex | Alignment Explorer With Multiple Devices | |

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

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

c.phylo | Building Lists of Trees | |

pic | Phylogenetically Independent Contrasts | |

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

kronoviz | Plot Multiple Chronograms on the Same Scale | |

where | Find Patterns in DNA Sequences | |

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

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

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

zoom | Zoom on a Portion of a Phylogeny | |

LTT | Theoretical Lineage-Through Time Plots | |

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

MPR | Most Parsimonious Reconstruction | |

bind.tree | Binds Trees | |

compar.lynch | Lynch's Comparative Method | |

summary.phylo | Print Summary of a Phylogeny | |

axisPhylo | Axis on Side of Phylogeny | |

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

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

which.edge | Identifies Edges of a Tree | |

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

boot.phylo | Tree Bipartition and Bootstrapping Phylogenies | |

stree | Generates Systematic Regular Trees | |

rtt | Root a Tree by Root-to-Tip Regression | |

diversi.gof | Tests of Constant Diversification Rates | |

howmanytrees | Calculate Numbers of Phylogenetic Trees | |

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

multi2di | Collapse and Resolve Multichotomies | |

gammaStat | Gamma-Statistic of Pybus and Harvey | |

compute.brtime | Compute and Set Branching Times | |

clustal | Multiple Sequence Alignment with External Applications | |

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

treePop | Tree Popping | |

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

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

rotate | Swapping Sister Clades | |

corClasses | Phylogenetic Correlation Structures | |

phymltest | Fits a Bunch of Models with PhyML | |

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

delta.plot | Delta Plots | |

carnivora | Carnivora body sizes and life history traits | |

dist.gene | Pairwise Distances from Genetic Data | |

ace | Ancestral Character Estimation | |

data.nex | NEXUS Data Example | |

varCompPhylip | Variance Components with Orthonormal Contrasts | |

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

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

compar.gee | Comparative Analysis with GEEs | |

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

base.freq | Base frequencies from DNA Sequences | |

lmorigin | Multiple regression through the origin | |

edges | Draw Additional Edges on a Plotted Tree | |

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

corBrownian | Brownian Correlation Structure | |

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

evonet | Evolutionary Networks | |

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

compar.cheverud | Cheverud's Comparative Method | |

makeNodeLabel | Makes Node Labels | |

additive | Incomplete Distance Matrix Filling | |

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

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

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

compute.brlen | Branch Lengths Computation | |

dist.topo | Topological Distances Between Two Trees | |

dist.dna | Pairwise Distances from DNA Sequences | |

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

chronopl | Molecular Dating With Penalized Likelihood | |

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

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

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

balance | Balance of a Dichotomous Phylogenetic Tree | |

chronoMPL | Molecular Dating With Mean Path Lengths | |

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

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

diversity.contrast.test | Diversity Contrast Test | |

ape-internal | Internal Ape Functions | |

as.bitsplits | Split Frequencies and Conversion Among Split Classes | |

chiroptera | Bat Phylogeny | |

collapsed.intervals | Collapsed Coalescent Intervals | |

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

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

parafit | Test of host-parasite coevolution | |

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

ltt.plot | Lineages Through Time Plot | |

mrca | Find Most Recent Common Ancestors Between Pairs | |

CADM.global | Congruence among distance matrices | |

mst | Minimum Spanning Tree | |

is.compatible | Check Compatibility of Splits | |

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

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

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

print.phylo | Compact Display of a Phylogeny | |

woodmouse | Cytochrome b Gene Sequences of Woodmice | |

plot.varcomp | Plot Variance Components | |

pic.ortho | Phylogenetically Independent Orthonormal Contrasts | |

unique.multiPhylo | Revomes Duplicate Trees | |

weight.taxo | Define Similarity Matrix | |

plot.correlogram | Plot a Correlogram | |

reorder.phylo | Internal Reordering of Trees | |

subtrees | All subtrees of a Phylogenetic Tree | |

multiphylo | Manipulating Lists of Trees | |

vcv | Phylogenetic Variance-covariance or Correlation Matrix | |

mvr | Minimum Variance Reduction | |

varcomp | Compute Variance Component Estimates | |

trex | Tree Explorer With Multiple Devices | |

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

rtree | Generates Random Trees | |

root | Roots Phylogenetic Trees | |

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

phydataplot | Tree Annotation | |

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

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

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

consensus | Concensus Trees | |

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

mat5M3ID | Five Trees | |

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

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

landplants | Gene Tree of 36 Landplant rbcL Sequences | |

rTraitCont | Continuous Character Simulation | |

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

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

matexpo | Matrix Exponential | |

mat3 | Three Matrices | |

makeLabel | Label Management | |

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

correlogram.formula | Phylogenetic Correlogram | |

image.DNAbin | Plot of DNA Sequence Alignement | |

mixedFontLabel | Mixed Font Labels for Plotting | |

mat5Mrand | Five Independent Trees | |

ladderize | Ladderize a Tree | |

is.monophyletic | Is Group Monophyletic | |

opsin | Gene Tree of 32 opsin Sequences | |

plot.phylo | Plot Phylogenies | |

pcoa | Principal Coordinate Analysis | |

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

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

nj | Neighbor-Joining Tree Estimation | |

rTraitDisc | Discrete Character Simulation | |

skyline | Skyline Plot Estimate of Effective Population Size | |

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

triangMtd | Tree Reconstruction Based on the Triangles Method | |

rTraitMult | Multivariate Character Simulation | |

skylineplot | Drawing Skyline Plot Graphs | |

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

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

speciesTree | Species Tree Estimation | |

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

No Results! |

## Last month downloads

## Details

Date | 2014-07-15 |

ZipData | no |

License | GPL (>= 2) |

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

Packaged | 2014-07-15 08:04:40 UTC; paradis |

NeedsCompilation | yes |

Repository | CRAN |

Date/Publication | 2014-07-15 11:13:25 |

depends | base (>= 3.0.0) , R (>= 3.0.0) |

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, Rosemary McCloskey |

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