ape v3.0-7

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