ape v3.1-4

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