# ape v3.0-1

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, analyses of diversification and
macroevolution, computing distances from allelic and nucleotide
data, reading nucleotide sequences, and several tools such as
Mantel's test, computation of minimum spanning tree,
generalized skyline plots, estimation of absolute evolutionary
rates and clock-like trees using mean path lengths,
non-parametric rate smoothing 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).

## Functions in ape

Name | Description | |

axisPhylo | Axis on Side of Phylogeny | |

compute.brlen | Branch Lengths Computation | |

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

GC.content | Content in GC from DNA Sequences | |

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

SDM | Construction of Consensus Distance Matrix With SDM | |

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

as.bitsplits | Conversion Among Split Classes | |

ape-internal | Internal Ape Functions | |

landplants | Gene Tree of 36 Landplant rbcL Sequences | |

mat5Mrand | Five Independent Trees | |

is.compatible | Check Compatibility of Splits | |

pic.ortho | Phylogenetically Independent Orthonormal Contrasts | |

treePop | Tree Popping | |

ladderize | Ladderize a Tree | |

print.phylo | Compact Display of a Phylogeny | |

additive | Incomplete Distance Matrix Filling | |

chronopl | Molecular Dating With Penalized Likelihood | |

multi2di | Collapse and Resolve Multichotomies | |

reorder.phylo | Internal Reordering of Trees | |

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

rTraitDisc | Discrete Character Simulation | |

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

edges | Draw Additional Edges on a Plotted Tree | |

chronoMPL | Molecular Dating With Mean Path Lengths | |

carnivora | Carnivora body sizes and life history traits | |

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

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

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

mvr | Minimum Variance Reduction | |

chiroptera | Bat Phylogeny | |

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

ape-defunct | Defunct Ape Functions | |

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

balance | Balance of a Dichotomous Phylogenetic Tree | |

data.nex | NEXUS Data Example | |

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

c.phylo | Building Lists of Trees | |

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

base.freq | Base frequencies from DNA Sequences | |

collapse.singles | Collapse Single Nodes | |

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

mat3 | Three Matrices | |

diversity.contrast.test | Diversity Contrast Test | |

opsin | Gene Tree of 32 opsin Sequences | |

stree | Generates Systematic Regular Trees | |

gammaStat | Gamma-Statistic of Pybus and Harvey | |

triangMtd | Tree Reconstruction Based on the Triangles Method | |

collapsed.intervals | Collapsed Coalescent Intervals | |

is.monophyletic | Is Group Monophyletic | |

matexpo | Matrix Exponential | |

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

mst | Minimum Spanning Tree | |

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

dist.topo | Topological Distances Between Two Trees | |

correlogram.formula | Phylogenetic Correlogram | |

clustal | Multiple Sequence Alignment with External Applications | |

dist.gene | Pairwise Distances from Genetic Data | |

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

MPR | Most Parsimonious Reconstruction | |

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

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

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

ape-package | Analyses of Phylogenetics and Evolution | |

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

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

summary.phylo | Print Summary of a Phylogeny | |

delta.plot | Delta Plots | |

nj | Neighbor-Joining Tree Estimation | |

mixedFontLabel | Mixed Font Labels for Plotting | |

compute.brtime | Compute and Set Branching Times | |

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

mat5M3ID | Five Trees | |

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

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

rotate | Swapping Sister Clades | |

kronoviz | Plot Multiple Chronograms on the Same Scale | |

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

diversi.gof | Tests of Constant Diversification Rates | |

where | Find Patterns in DNA Sequences | |

subtrees | All subtrees of a Phylogenetic Tree | |

varcomp | Compute Variance Component Estimates | |

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

weight.taxo | Define Similarity Matrix | |

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

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

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

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

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

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

mrca | Find Most Recent Common Ancestors Between Pairs | |

vcv | Phylogenetic Variance-covariance or Correlation Matrix | |

coalescent.intervals | Coalescent Intervals | |

evonet | Evolutionary Networks | |

unique.multiPhylo | Revomes Duplicate Trees | |

plot.correlogram | Plot a Correlogram | |

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

alex | Alignment Explorer With Multiple Devices | |

skylineplot | Drawing Skyline Plot Graphs | |

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

rTraitCont | Continuous Character Simulation | |

corClasses | Phylogenetic Correlation Structures | |

consensus | Concensus Trees | |

makeLabel | Label Management | |

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

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

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

pic | Phylogenetically Independent Contrasts | |

root | Roots Phylogenetic Trees | |

skyline | Skyline Plot Estimate of Effective Population Size | |

CADM.global | Congruence among distance matrices | |

corBrownian | Brownian Correlation Structure | |

ace | Ancestral Character Estimation | |

plot.varcomp | Plot Variance Components | |

multiphylo | Manipulating Lists of Trees | |

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

howmanytrees | Calculate Numbers of Phylogenetic Trees | |

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

rtree | Generates Random Trees | |

zoom | Zoom on a Portion of a Phylogeny | |

bind.tree | Binds Trees | |

rTraitMult | Multivariate Character Simulation | |

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

which.edge | Identifies Edges of a Tree | |

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

pcoa | Principal Coordinate Analysis | |

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

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

compar.gee | Comparative Analysis with GEEs | |

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

image.DNAbin | Plot of DNA Sequence Alignement | |

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

ltt.plot | Lineages Through Time Plot | |

compar.lynch | Lynch's Comparative Method | |

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

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

makeNodeLabel | Makes Node Labels | |

lmorigin | Multiple regression through the origin | |

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

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

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

node.depth | Depth of Nodes and Tips | |

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

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

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

varCompPhylip | Variance Components with Orthonormal Contrasts | |

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

boot.phylo | Tree Bipartition and Bootstrapping Phylogenies | |

woodmouse | Cytochrome b Gene Sequences of Woodmice | |

dist.dna | Pairwise Distances from DNA Sequences | |

phymltest | Fits a Bunch of Models with PhyML | |

parafit | Test of host-parasite coevolution | |

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

compar.cheverud | Cheverud's Comparative Method | |

trex | Tree Explorer With Multiple Devices | |

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

speciesTree | Species Tree Estimation | |

plot.phylo | Plot Phylogenies | |

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

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

No Results! |

## Last month downloads

## Details

Date | 2012-02-17 |

ZipData | no |

License | GPL (>= 2) |

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

Packaged | 2012-02-20 07:59:43 UTC; paradis |

Repository | CRAN |

Date/Publication | 2012-02-20 09:24:49 |

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