ape v3.0-2

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