# ape v3.0-4

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,
minimum spanning tree, 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 | |

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

clustal | Multiple Sequence Alignment with External Applications | |

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

additive | Incomplete Distance Matrix Filling | |

MPR | Most Parsimonious Reconstruction | |

corClasses | Phylogenetic Correlation Structures | |

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

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

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

c.phylo | Building Lists of Trees | |

balance | Balance of a Dichotomous Phylogenetic Tree | |

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

as.bitsplits | Conversion Among Split Classes | |

ape-internal | Internal Ape Functions | |

axisPhylo | Axis on Side of Phylogeny | |

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

pic.ortho | Phylogenetically Independent Orthonormal Contrasts | |

coalescent.intervals | Coalescent Intervals | |

rTraitCont | Continuous Character Simulation | |

consensus | Concensus Trees | |

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

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

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

CADM.global | Congruence among distance matrices | |

edges | Draw Additional Edges on a Plotted Tree | |

multiphylo | Manipulating Lists of Trees | |

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

mvr | Minimum Variance Reduction | |

rTraitDisc | Discrete Character Simulation | |

which.edge | Identifies Edges of a Tree | |

print.phylo | Compact Display of a Phylogeny | |

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

reorder.phylo | Internal Reordering of Trees | |

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

mst | Minimum Spanning Tree | |

opsin | Gene Tree of 32 opsin Sequences | |

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

rotate | Swapping sister clades | |

plot.varcomp | Plot Variance Components | |

unique.multiPhylo | Revomes Duplicate Trees | |

is.compatible | Check Compatibility of Splits | |

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

collapsed.intervals | Collapsed Coalescent Intervals | |

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

ape-package | Analyses of Phylogenetics and Evolution | |

speciesTree | Species Tree Estimation | |

makeNodeLabel | Makes Node Labels | |

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

nj | Neighbor-Joining Tree Estimation | |

mat5Mrand | Five Independent Trees | |

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

pcoa | Principal Coordinate Analysis | |

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

trex | Tree Explorer With Multiple Devices | |

mat5M3ID | Five Trees | |

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

base.freq | Base frequencies from DNA Sequences | |

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

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

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

chiroptera | Bat Phylogeny | |

mat3 | Three Matrices | |

bind.tree | Binds Trees | |

SDM | Construction of Consensus Distance Matrix With SDM | |

mrca | Find Most Recent Common Ancestors Between Pairs | |

carnivora | Carnivora body sizes and life history traits | |

summary.phylo | Print Summary of a Phylogeny | |

dist.gene | Pairwise Distances from Genetic Data | |

matexpo | Matrix Exponential | |

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

compar.cheverud | Cheverud's Comparative Method | |

diversi.gof | Tests of Constant Diversification Rates | |

varCompPhylip | Variance Components with Orthonormal Contrasts | |

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

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

varcomp | Compute Variance Component Estimates | |

weight.taxo | Define Similarity Matrix | |

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

compar.lynch | Lynch's Comparative Method | |

kronoviz | Plot Multiple Chronograms on the Same Scale | |

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

woodmouse | Cytochrome b Gene Sequences of Woodmice | |

zoom | Zoom on a Portion of a Phylogeny | |

delta.plot | Delta Plots | |

image.DNAbin | Plot of DNA Sequence Alignement | |

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

correlogram.formula | Phylogenetic Correlogram | |

parafit | Test of host-parasite coevolution | |

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

data.nex | NEXUS Data Example | |

gammaStat | Gamma-Statistic of Pybus and Harvey | |

pic | Phylogenetically Independent Contrasts | |

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

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

is.monophyletic | Is Group Monophyletic | |

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

chronoMPL | Molecular Dating With Mean Path Lengths | |

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

multi2di | Collapse and Resolve Multichotomies | |

alex | Alignment Explorer With Multiple Devices | |

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

plot.correlogram | Plot a Correlogram | |

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

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

root | Roots Phylogenetic Trees | |

rTraitMult | Multivariate Character Simulation | |

vcv | Phylogenetic Variance-covariance or Correlation Matrix | |

collapse.singles | Collapse Single Nodes | |

mixedFontLabel | Mixed Font Labels for Plotting | |

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

stree | Generates Systematic Regular Trees | |

triangMtd | Tree Reconstruction Based on the Triangles Method | |

ladderize | Ladderize a Tree | |

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

phymltest | Fits a Bunch of Models with PhyML | |

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

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

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

corBrownian | Brownian Correlation Structure | |

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

node.depth | Depth of Nodes and Tips | |

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

subtrees | All subtrees of a Phylogenetic Tree | |

plot.phylo | Plot Phylogenies | |

treePop | Tree Popping | |

ace | Ancestral Character Estimation | |

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

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

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

chronopl | Molecular Dating With Penalized Likelihood | |

ltt.plot | Lineages Through Time Plot | |

skyline | Skyline Plot Estimate of Effective Population Size | |

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

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

rtree | Generates Random Trees | |

boot.phylo | Tree Bipartition and Bootstrapping Phylogenies | |

compute.brtime | Compute and Set Branching Times | |

landplants | Gene Tree of 36 Landplant rbcL Sequences | |

compar.gee | Comparative Analysis with GEEs | |

makeLabel | Label Management | |

compute.brlen | Branch Lengths Computation | |

skylineplot | Drawing Skyline Plot Graphs | |

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

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

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

howmanytrees | Calculate Numbers of Phylogenetic Trees | |

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

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

lmorigin | Multiple regression through the origin | |

evonet | Evolutionary Networks | |

diversity.contrast.test | Diversity Contrast Test | |

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

dist.topo | Topological Distances Between Two Trees | |

dist.dna | Pairwise Distances from DNA Sequences | |

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

No Results! |

## Last month downloads

## Details

Date | 2012-05-03 |

ZipData | no |

License | GPL (>= 2) |

URL | http://ape.mpl.ird.fr/ |

Packaged | 2012-06-13 03:38:28 UTC; paradis |

Repository | CRAN |

Date/Publication | 2012-08-01 09:03:41 |

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