ape v3.0-5

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