ape v3.0-1


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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, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method).

Functions in ape

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