ape v3.0-11


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