ape v2.8

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