ape v3.0-6

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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, ancestral character analyses, analyses of diversification and macroevolution, computing distances from allelic and nucleotide data, reading and writing nucleotide sequences, and several tools such as Mantel's test, minimum spanning tree, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths 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). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.

Functions in ape

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