ape v3.0-10

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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
bird.orders Phylogeny of the Orders of Birds From Sibley and Ahlquist
as.alignment Conversion Among DNA Sequence Internal Formats
additive Incomplete Distance Matrix Filling
all.equal.phylo Global Comparison of two Phylogenies
BIONJ Tree Estimation Based on an Improved Version of the NJ Algorithm
MPR Most Parsimonious Reconstruction
alex Alignment Explorer With Multiple Devices
ape-internal Internal Ape Functions
slowinskiguyer.test Slowinski-Guyer Test of Homogeneous Diversification
bd.time Time-Dependent Birth-Death Models
bd.ext Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
coalescent.intervals Coalescent Intervals
bind.tree Binds Trees
branching.times Branching Times of a Phylogenetic Tree
Initialize.corPhyl Initialize a `corPhyl' Structure Object
balance Balance of a Dichotomous Phylogenetic Tree
mrca Find Most Recent Common Ancestors Between Pairs
birthdeath Estimation of Speciation and Extinction Rates With Birth-Death Models
as.bitsplits Conversion Among Split Classes
is.binary.tree Test for Binary Tree
axisPhylo Axis on Side of Phylogeny
Moran.I Moran's I Autocorrelation Index
compar.cheverud Cheverud's Comparative Method
is.monophyletic Is Group Monophyletic
njs Tree Reconstruction from Incomplete Distances With NJ* or bio-NJ*
c.phylo Building Lists of Trees
chronos Molecular Dating by Penalised Likelihood and Maximum Likelihood
mixedFontLabel Mixed Font Labels for Plotting
chiroptera Bat Phylogeny
read.nexus.data Read Character Data In NEXUS Format
corPagel Pagel's ``lambda'' Correlation Structure
yule Fits the Yule Model to a Phylogenetic Tree
mantel.test Mantel Test for Similarity of Two Matrices
mat3 Three Matrices
kronoviz Plot Multiple Chronograms on the Same Scale
chronoMPL Molecular Dating With Mean Path Lengths
edges Draw Additional Edges on a Plotted Tree
mat5Mrand Five Independent Trees
write.tree Write Tree File in Parenthetic Format
FastME Tree Estimation Based on the Minimum Evolution Algorithm
matexpo Matrix Exponential
ladderize Ladderize a Tree
is.ultrametric Test if a Tree is Ultrametric
bird.families Phylogeny of the Families of Birds From Sibley and Ahlquist
summary.phylo Print Summary of a Phylogeny
skyline Skyline Plot Estimate of Effective Population Size
pcoa Principal Coordinate Analysis
as.phylo.formula Conversion from Taxonomy Variables to Phylogenetic Trees
landplants Gene Tree of 36 Landplant rbcL Sequences
read.nexus Read Tree File in Nexus Format
collapse.singles Collapse Single Nodes
clustal Multiple Sequence Alignment with External Applications
evonet Evolutionary Networks
plot.varcomp Plot Variance Components
corMartins Martins's (1997) Correlation Structure
rtree Generates Random Trees
richness.yule.test Test of Diversification-Shift With the Yule Process
rTraitCont Continuous Character Simulation
read.GenBank Read DNA Sequences from GenBank via Internet
is.compatible Check Compatibility of Splits
seg.sites Find Segregating Sites in DNA Sequences
unique.multiPhylo Revomes Duplicate Trees
write.nexus.data Write Character Data in NEXUS Format
where Find Patterns in DNA Sequences
yule.time Fits the Time-Dependent Yule Model
ewLasso Incomplete distances and edge weights of unrooted topology
rTraitMult Multivariate Character Simulation
corBrownian Brownian Correlation Structure
triangMtd Tree Reconstruction Based on the Triangles Method
mcconwaysims.test McConway-Sims Test of Homogeneous Diversification
as.matching Conversion Between Phylo and Matching Objects
multiphylo Manipulating Lists of Trees
which.edge Identifies Edges of a Tree
print.phylo Compact Display of a Phylogeny
write.nexus Write Tree File in Nexus Format
woodmouse Cytochrome b Gene Sequences of Woodmice
as.phylo Conversion Among Tree and Network Objects
node.depth Depth and Heights of Nodes and Tips
pic.ortho Phylogenetically Independent Orthonormal Contrasts
mcmc.popsize Reversible Jump MCMC to Infer Demographic History
boot.phylo Tree Bipartition and Bootstrapping Phylogenies
subtrees All subtrees of a Phylogenetic Tree
corGrafen Grafen's (1989) Correlation Structure
add.scale.bar Add a Scale Bar to a Phylogeny Plot
ltt.plot Lineages Through Time Plot
cherry Number of Cherries and Null Models of Trees
cophenetic.phylo Pairwise Distances from a Phylogenetic Tree
hivtree Phylogenetic Tree of 193 HIV-1 Sequences
base.freq Base frequencies from DNA Sequences
ape-package Analyses of Phylogenetics and Evolution
howmanytrees Calculate Numbers of Phylogenetic Trees
read.caic Read Tree File in CAIC Format
identify.phylo Graphical Identification of Nodes and Tips
treePop Tree Popping
root Roots Phylogenetic Trees
rlineage Tree Simulation Under the Time-Dependent Birth--Death Models
trex Tree Explorer With Multiple Devices
skylineplot Drawing Skyline Plot Graphs
SDM Construction of Consensus Distance Matrix With SDM
weight.taxo Define Similarity Matrix
speciesTree Species Tree Estimation
makeNodeLabel Makes Node Labels
zoom Zoom on a Portion of a Phylogeny
chronopl Molecular Dating With Penalized Likelihood
makeLabel Label Management
image.DNAbin Plot of DNA Sequence Alignement
carnivora Carnivora body sizes and life history traits
compar.lynch Lynch's Comparative Method
nj Neighbor-Joining Tree Estimation
gammaStat Gamma-Statistic of Pybus and Harvey
consensus Concensus Trees
mvr Minimum Variance Reduction
pic Phylogenetically Independent Contrasts
corClasses Phylogenetic Correlation Structures
DNAbin Manipulate DNA Sequences in Bit-Level Format
stree Generates Systematic Regular Trees
subtreeplot Zoom on a Portion of a Phylogeny by Successive Clicks
lmorigin Multiple regression through the origin
write.dna Write DNA Sequences in a File
read.dna Read DNA Sequences in a File
read.tree Read Tree File in Parenthetic Format
nodelabels Labelling the Nodes, Tips, and Edges of a Tree
opsin Gene Tree of 32 opsin Sequences
diversi.gof Tests of Constant Diversification Rates
multi2di Collapse and Resolve Multichotomies
mst Minimum Spanning Tree
vcv Phylogenetic Variance-covariance or Correlation Matrix
collapsed.intervals Collapsed Coalescent Intervals
rotate Swapping Sister Clades
del.gaps Delete Alignment Gaps in DNA Sequences
varcomp Compute Variance Component Estimates
ace Ancestral Character Estimation
compar.gee Comparative Analysis with GEEs
CADM.global Congruence among distance matrices
reorder.phylo Internal Reordering of Trees
varCompPhylip Variance Components with Orthonormal Contrasts
dist.dna Pairwise Distances from DNA Sequences
phymltest Fits a Bunch of Models with PhyML
plot.phylo Plot Phylogenies
mat5M3ID Five Trees
plot.correlogram Plot a Correlogram
yule.cov Fits the Yule Model With Covariates
rTraitDisc Discrete Character Simulation
parafit Test of host-parasite coevolution
correlogram.formula Phylogenetic Correlogram
dist.gene Pairwise Distances from Genetic Data
delta.plot Delta Plots
cophyloplot Plots two phylogenetic trees face to face with links between the tips.
diversi.time Analysis of Diversification with Survival Models
corBlomberg Blomberg et al.'s Correlation Structure
dist.topo Topological Distances Between Two Trees
data.nex NEXUS Data Example
dbd Probability Density Under Birth--Death Models
compute.brtime Compute and Set Branching Times
compar.ou Ornstein--Uhlenbeck Model for Continuous Characters
compute.brlen Branch Lengths Computation
diversity.contrast.test Diversity Contrast Test
drop.tip Remove Tips in a Phylogenetic Tree
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