# ape v4.0

Monthly downloads

## Analyses of Phylogenetics and Evolution

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 DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, 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, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. 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, MAFFT) whose results are returned into R.

## Functions in ape

Name | Description | |

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

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

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

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

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

axisPhylo | Axis on Side of Phylogeny | |

balance | Balance of a Dichotomous Phylogenetic Tree | |

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

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

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

base.freq | Base frequencies from DNA Sequences | |

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

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

c.phylo | Building Lists of Trees | |

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

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

bind.tree | Binds Trees | |

carnivora | Carnivora body sizes and life history traits | |

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

CADM.global | Congruence among distance matrices | |

boot.phylo | Tree Bipartition and Bootstrapping Phylogenies | |

checkAlignment | Check DNA Alignments | |

checkValidPhylo | Check the Structure of a "phylo" Object | |

clustal | Multiple Sequence Alignment with External Applications | |

chronoMPL | Molecular Dating With Mean Path Lengths | |

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

collapse.singles | Collapse Single Nodes | |

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

coalescent.intervals | Coalescent Intervals | |

chronopl | Molecular Dating With Penalized Likelihood | |

chiroptera | Bat Phylogeny | |

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

compute.brlen | Branch Lengths Computation | |

compar.cheverud | Cheverud's Comparative Method | |

collapsed.intervals | Collapsed Coalescent Intervals | |

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

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

consensus | Concensus Trees | |

compute.brtime | Compute and Set Branching Times | |

compar.gee | Comparative Analysis with GEEs | |

corClasses | Phylogenetic Correlation Structures | |

compar.lynch | Lynch's Comparative Method | |

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

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

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

dist.topo | Topological Distances Between Two Trees | |

data.nex | NEXUS Data Example | |

correlogram.formula | Phylogenetic Correlogram | |

diversi.gof | Tests of Constant Diversification Rates | |

evonet | Evolutionary Networks | |

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

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

def | Definition of Vectors for Plotting or Annotating | |

lmorigin | Multiple regression through the origin | |

DNAbin2indel | Recode Blocks of Indels | |

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

dist.dna | Pairwise Distances from DNA Sequences | |

LTT | Theoretical Lineage-Through Time Plots | |

dist.gene | Pairwise Distances from Genetic Data | |

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

image.DNAbin | Plot of DNA Sequence Alignement | |

label2table | Label Management | |

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

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

ladderize | Ladderize a Tree | |

mvr | Minimum Variance Reduction | |

multiphylo | Manipulating Lists of Trees | |

ltt.plot | Lineages Through Time Plot | |

node.dating | node.dating | |

makeLabel | Label Management | |

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

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

print.phylo | Compact Display of a Phylogeny | |

rTraitDisc | Discrete Character Simulation | |

rTraitCont | Continuous Character Simulation | |

alex | Alignment Explorer With Multiple Devices | |

all.equal.DNAbin | Compare DNA Sets | |

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

corBrownian | Brownian Correlation Structure | |

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

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

diversity.contrast.test | Diversity Contrast Test | |

gammaStat | Gamma-Statistic of Pybus and Harvey | |

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

kronoviz | Plot Multiple Chronograms on the Same Scale | |

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

skylineplot | Drawing Skyline Plot Graphs | |

treePop | Tree Popping | |

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

trex | Tree Explorer With Multiple Devices | |

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

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

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

alview | Print DNA or AA Sequence Alignement | |

multi2di | Collapse and Resolve Multichotomies | |

mst | Minimum Spanning Tree | |

pic.ortho | Phylogenetically Independent Orthonormal Contrasts | |

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

plot.correlogram | Plot a Correlogram | |

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

reconstruct | Continuous Ancestral Character Estimation | |

ape-internal | Internal Ape Functions | |

rTraitMult | Multivariate Character Simulation | |

reorder.phylo | Internal Reordering of Trees | |

ape-package | Analyses of Phylogenetics and Evolution | |

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

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

edges | Draw Additional Edges on a Plotted Tree | |

mat3 | Three Matrices | |

is.binary | Test for Binary Tree | |

mat5M3ID | Five Trees | |

mat5Mrand | Five Independent Trees | |

mixedFontLabel | Mixed Font Labels for Plotting | |

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

mrca | Find Most Recent Common Ancestors Between Pairs | |

MPR | Most Parsimonious Reconstruction | |

matexpo | Matrix Exponential | |

read.gff | Read GFF Files | |

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

root | Roots Phylogenetic Trees | |

trans | Translation from DNA to Amino Acid Sequences | |

rotate | Swapping Sister Clades | |

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

summary.phylo | Print Summary of a Phylogeny | |

subtrees | All subtrees of a Phylogenetic Tree | |

rtree | Generates Random Trees | |

woodmouse | Cytochrome b Gene Sequences of Woodmice | |

which.edge | Identifies Edges of a Tree | |

AAbin | Amino Acid Sequences | |

ace | Ancestral Character Estimation | |

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

nodepath | Find Paths of Nodes | |

plot.phylo.extra | Extra Fuctions to Plot and Annotate Phylogenies | |

plot.phylo | Plot Phylogenies | |

unique.multiPhylo | Revomes Duplicate Trees | |

triangMtd | Tree Reconstruction Based on the Triangles Method | |

speciesTree | Species Tree Estimation | |

stree | Generates Systematic Regular Trees | |

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

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

vcv | Phylogenetic Variance-covariance or Correlation Matrix | |

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

vcv2phylo | Variance-Covariance Matrix to Tree | |

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

delta.plot | Delta Plots | |

additive | Incomplete Distance Matrix Filling | |

is.compatible | Check Compatibility of Splits | |

howmanytrees | Calculate Numbers of Phylogenetic Trees | |

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

is.monophyletic | Is Group Monophyletic | |

makeNodeLabel | Makes Node Labels | |

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

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

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

pic | Phylogenetically Independent Contrasts | |

phymltest | Fits a Bunch of Models with PhyML | |

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

varcomp | Compute Variance Component Estimates | |

SDM | Construction of Consensus Distance Matrix With SDM | |

varCompPhylip | Variance Components with Orthonormal Contrasts | |

weight.taxo | Define Similarity Matrix | |

where | Find Patterns in DNA Sequences | |

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

parafit | Test of host-parasite coevolution | |

nj | Neighbor-Joining Tree Estimation | |

plot.varcomp | Plot Variance Components | |

phydataplot | Tree Annotation | |

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

plotTreeTime | Plot Tree With Time Axis | |

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

skyline | Skyline Plot Estimate of Effective Population Size | |

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

zoom | Zoom on a Portion of a Phylogeny | |

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

No Results! |

## Last month downloads

## Details

Date | 2016-11-29 |

ZipData | no |

License | GPL (>= 2) |

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

NeedsCompilation | yes |

Packaged | 2016-11-30 09:33:29 UTC; paradis |

Repository | CRAN |

Date/Publication | 2016-12-01 17:40:32 |

suggests | expm , gee |

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

depends | R (>= 3.2.0) |

Contributors | Anthony Ives, 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, Simon Blomberg, Gilles Didier, Manuela Royer-Carenzi, Bradley Jones |

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