ape v2.5-3

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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, analyses of diversification and macroevolution, computing distances from allelic and nucleotide data, reading nucleotide sequences, and several tools such as Mantel's test, computation of minimum spanning tree, generalized skyline plots, estimation of absolute evolutionary rates and clock-like trees using mean path lengths, non-parametric rate smoothing and penalized likelihood. Phylogeny estimation can be done with the NJ, BIONJ, and ME methods.

Functions in ape

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