ape v3.0-4

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