ape v3.0-8

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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
as.phylo.formula Conversion from Taxonomy Variables to Phylogenetic Trees
ape-package Analyses of Phylogenetics and Evolution
BIONJ Tree Estimation Based on an Improved Version of the NJ Algorithm
rTraitCont Continuous Character Simulation
unique.multiPhylo Revomes Duplicate Trees
chronoMPL Molecular Dating With Mean Path Lengths
opsin Gene Tree of 32 opsin Sequences
Initialize.corPhyl Initialize a `corPhyl' Structure Object
data.nex NEXUS Data Example
balance Balance of a Dichotomous Phylogenetic Tree
collapse.singles Collapse Single Nodes
as.alignment Conversion Among DNA Sequence Internal Formats
gammaStat Gamma-Statistic of Pybus and Harvey
compar.cheverud Cheverud's Comparative Method
correlogram.formula Phylogenetic Correlogram
corBrownian Brownian Correlation Structure
phymltest Fits a Bunch of Models with PhyML
howmanytrees Calculate Numbers of Phylogenetic Trees
is.ultrametric Test if a Tree is Ultrametric
mantel.test Mantel Test for Similarity of Two Matrices
corGrafen Grafen's (1989) Correlation Structure
corMartins Martins's (1997) Correlation Structure
mat5M3ID Five Trees
additive Incomplete Distance Matrix Filling
mat5Mrand Five Independent Trees
is.binary.tree Test for Binary Tree
pic Phylogenetically Independent Contrasts
njs Tree Reconstruction from Incomplete Distances With NJ* or bio-NJ*
corClasses Phylogenetic Correlation Structures
corBlomberg Blomberg et al.'s Correlation Structure
chiroptera Bat Phylogeny
is.compatible Check Compatibility of Splits
FastME Tree Estimation Based on the Minimum Evolution Algorithm
plot.correlogram Plot a Correlogram
hivtree Phylogenetic Tree of 193 HIV-1 Sequences
nj Neighbor-Joining Tree Estimation
CADM.global Congruence among distance matrices
branching.times Branching Times of a Phylogenetic Tree
triangMtd Tree Reconstruction Based on the Triangles Method
rlineage Tree Simulation Under the Time-Dependent Birth--Death Models
yule.time Fits the Time-Dependent Yule Model
skylineplot Drawing Skyline Plot Graphs
ape-internal Internal Ape Functions
skyline Skyline Plot Estimate of Effective Population Size
evonet Evolutionary Networks
coalescent.intervals Coalescent Intervals
print.phylo Compact Display of a Phylogeny
compute.brtime Compute and Set Branching Times
compar.lynch Lynch's Comparative Method
diversi.time Analysis of Diversification with Survival Models
root Roots Phylogenetic Trees
nodelabels Labelling the Nodes, Tips, and Edges of a Tree
rTraitMult Multivariate Character Simulation
dist.topo Topological Distances Between Two Trees
subtrees All subtrees of a Phylogenetic Tree
node.depth Depth and Heights of Nodes and Tips
SDM Construction of Consensus Distance Matrix With SDM
identify.phylo Graphical Identification of Nodes and Tips
read.nexus Read Tree File in Nexus Format
compute.brlen Branch Lengths Computation
collapsed.intervals Collapsed Coalescent Intervals
base.freq Base frequencies from DNA Sequences
diversi.gof Tests of Constant Diversification Rates
rtree Generates Random Trees
consensus Concensus Trees
add.scale.bar Add a Scale Bar to a Phylogeny Plot
is.monophyletic Is Group Monophyletic
mcconwaysims.test McConway-Sims Test of Homogeneous Diversification
kronoviz Plot Multiple Chronograms on the Same Scale
bird.orders Phylogeny of the Orders of Birds From Sibley and Ahlquist
mixedFontLabel Mixed Font Labels for Plotting
trex Tree Explorer With Multiple Devices
subtreeplot Zoom on a Portion of a Phylogeny by Successive Clicks
ewLasso Incomplete distances and edge weights of unrooted topology
speciesTree Species Tree Estimation
read.nexus.data Read Character Data In NEXUS Format
bd.time Time-Dependent Birth-Death Models
weight.taxo Define Similarity Matrix
as.matching Conversion Between Phylo and Matching Objects
landplants Gene Tree of 36 Landplant rbcL Sequences
read.caic Read Tree File in CAIC Format
write.nexus.data Write Character Data In NEXUS Format
seg.sites Find Segregating Sites in DNA Sequences
woodmouse Cytochrome b Gene Sequences of Woodmice
multiphylo Manipulating Lists of Trees
summary.phylo Print Summary of a Phylogeny
write.tree Write Tree File in Parenthetic Format
bd.ext Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
plot.varcomp Plot Variance Components
yule.cov Fits the Yule Model With Covariates
boot.phylo Tree Bipartition and Bootstrapping Phylogenies
alex Alignment Explorer With Multiple Devices
cophyloplot Plots two phylogenetic trees face to face with links between the tips.
mat3 Three Matrices
dist.gene Pairwise Distances from Genetic Data
dbd Probability Density Under Birth--Death Models
all.equal.phylo Global Comparison of two Phylogenies
Moran.I Moran's I Autocorrelation Index
carnivora Carnivora body sizes and life history traits
axisPhylo Axis on Side of Phylogeny
write.nexus Write Tree File in Nexus Format
vcv Phylogenetic Variance-covariance or Correlation Matrix
plot.phylo Plot Phylogenies
makeLabel Label Management
reorder.phylo Internal Reordering of Trees
read.GenBank Read DNA Sequences from GenBank via Internet
image.DNAbin Plot of DNA Sequence Alignement
compar.ou Ornstein--Uhlenbeck Model for Continuous Characters
birthdeath Estimation of Speciation and Extinction Rates With Birth-Death Models
rTraitDisc Discrete Character Simulation
bind.tree Binds Trees
corPagel Pagel's ``lambda'' Correlation Structure
richness.yule.test Test of Diversification-Shift With the Yule Process
as.bitsplits Conversion Among Split Classes
matexpo Matrix Exponential
bird.families Phylogeny of the Families of Birds From Sibley and Ahlquist
stree Generates Systematic Regular Trees
mvr Minimum Variance Reduction
ladderize Ladderize a Tree
which.edge Identifies Edges of a Tree
rotate Swapping sister clades
yule Fits the Yule Model to a Phylogenetic Tree
DNAbin Manipulate DNA Sequences in Bit-Level Format
MPR Most Parsimonious Reconstruction
pic.ortho Phylogenetically Independent Orthonormal Contrasts
makeNodeLabel Makes Node Labels
treePop Tree Popping
c.phylo Building Lists of Trees
slowinskiguyer.test Slowinski-Guyer Test of Homogeneous Diversification
pcoa Principal Coordinate Analysis
clustal Multiple Sequence Alignment with External Applications
parafit Test of host-parasite coevolution
read.dna Read DNA Sequences in a File
zoom Zoom on a Portion of a Phylogeny
del.gaps Delete Alignment Gaps in DNA Sequences
edges Draw Additional Edges on a Plotted Tree
dist.dna Pairwise Distances from DNA Sequences
multi2di Collapse and Resolve Multichotomies
ace Ancestral Character Estimation
as.phylo Conversion Among Tree and Network Objects
compar.gee Comparative Analysis with GEEs
mcmc.popsize Reversible Jump MCMC to Infer Demographic History
cophenetic.phylo Pairwise Distances from a Phylogenetic Tree
varCompPhylip Variance Components with Orthonormal Contrasts
diversity.contrast.test Diversity Contrast Test
ltt.plot Lineages Through Time Plot
read.tree Read Tree File in Parenthetic Format
chronopl Molecular Dating With Penalized Likelihood
write.dna Write DNA Sequences in a File
mrca Find Most Recent Common Ancestors Between Pairs
chronos Molecular Dating by Penalised Likelihood and Maximum Likelihood
mst Minimum Spanning Tree
drop.tip Remove Tips in a Phylogenetic Tree
where Find Patterns in DNA Sequences
delta.plot Delta Plots
cherry Number of Cherries and Null Models of Trees
varcomp Compute Variance Component Estimates
lmorigin Multiple regression through the origin
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Date 2013-04-02
ZipData no
License GPL (>= 2)
URL http://ape.mpl.ird.fr/
Packaged 2013-04-02 08:53:05 UTC; paradis
NeedsCompilation yes
Repository CRAN
Date/Publication 2013-04-02 12:35:15

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