ape v2.7-2


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