ape v2.7-3

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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, and ME methods.

Functions in ape

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