ape v2.4-1


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