ape v3.1-2


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