ape v2.7-1

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