ape v2.6-3

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