ape v2.3-3

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