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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, classifying genes in trees using the Klastorin-Misawa-Tajima approach. Phylogeny estimation can be done with the NJ, BIONJ, ME, and ML methods.

Functions in ape

Name Description
ape-internal Internal Ape Functions
add.scale.bar Add a Scale Bar to a Phylogeny Plot
NPRS.criterion Objective Function Employed in Nonparametric Rate Smoothing
branching.times Branching Times of a Phylogenetic Tree
bird.families Phylogeny of the Families of Birds From Sibley and Ahlquist
balance Balance of a Dichotomous Phylogenetic Tree
compute.brlen Branch Lengths Computation
bind.tree Binds Trees
Moran.I Moran's I Autocorrelation Index
birthdeath Estimation of Speciation and Extinction Rates With Birth-Death Models
Initialize.corPhyl Initialize a 'corPhyl' Structure Object
bd.ext Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
all.equal.phylo Global Comparison of two Phylogenies
carnivora Carnivora body sizes and life history traits
chiroptera Bat Phylogeny
compar.lynch Lynch's Comparative Method
heterozygosity Heterozygosity at a Locus Using Gene Frequencies
bird.orders Phylogeny of the Orders of Birds From Sibley and Ahlquist
as.matching Conversion Between Phylo and Matching Objects
chronogram Chronogram Computed by Nonparametric Rate Smoothing
diversi.gof Tests of Constant Diversification Rates
write.dna Write DNA Sequences in a File
phymltest Fits a Bunch of Models with PHYML
DNAmodel Defines Models of DNA Evolution
weight.taxo Define Similarity Matrix
chronoMPL Molecular Dating With Mean Path Lengths
as.phylo.formula Conversion from Taxonomy Variables to Phylogenetic Trees
FastME Tree Estimation Based on the Minimum Evolution Algorithm
cherry Number of Cherries and Null Models of Trees
BIONJ Tree Estimation Based on an Improved Version of the NJ Algorithm
as.alignment Conversion Among DNA Sequence Internal Formats
DNAbin Manipulate DNA Sequences in Bit-Level Format
ace Ancestral Character Estimation
hivtree Phylogenetic Tree of 193 HIV-1 Sequences
pic Phylogenetically Independent Contrasts
dist.dna Pairwise Distances from DNA Sequences
nj Neighbor-Joining Tree Estimation
corMartins Martins's (1997) Correlation Structure
rtree Generates Random Trees
consensus Concensus Trees
seg.sites Find Segregating Sites in DNA Sequences
boot.phylo Tree Bipartition and Bootstrapping Phylogenies
as.phylo Conversion Among Tree Objects
evolve.phylo Ancestral Character Simulation
read.dna Read DNA Sequences in a File
GC.content Content in GC from DNA Sequences
dist.gene Pairwise Distances from Genetic Data
compar.cheverud Cheverud's Comparative Method
axisPhylo Axis on Side of Phylogeny
base.freq Base frequencies from DNA Sequences
corGrafen Grafen's (1989) Correlation Structure
ltt.plot Lineages Through Time Plot
root Roots Phylogenetic Trees
mrca Find Most Recent Common Ancestors Between Pairs
skyline Skyline Plot Estimate of Effective Population Size
compar.gee Comparative Analysis with GEEs
corBrownian Brownian Correlation Structure
plot.correlogram Plot a Correlogram
collapse.singles Collapse Single Nodes
write.nexus Write Tree File in Nexus Format
yule Fits Yule Model to a Phylogenetic Tree
identify.phylo Graphical Identification of Nodes and Tips
dist.topo Topological Distances Between Two Trees
is.binary.tree Test for Binary Tree
theta.h Population Parameter THETA using Homozygosity
diversi.time Analysis of Diversification with Survival Models
cophenetic.phylo Pairwise Distances from a Phylogenetic Tree
coalescent.intervals Coalescent Intervals
read.caic Read Tree File in CAIC Format
matexpo Matrix Exponential
is.ultrametric Test if a Tree is Ultrametric
node.depth Depth of Nodes and Tips
drop.tip Remove Tips in a Phylogenetic Tree
mcmc.popsize Reversible Jump MCMC to Infer Demographic History
read.nexus.data Read Character Data In NEXUS Format
read.nexus Read Tree File in Nexus Format
opsin Gene Tree of 32 opsin Sequences
klastorin Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000)
reorder.phylo Internal Reordering of Trees
nuc.div Nucleotide Diversity
compar.ou Ornstein--Uhlenbeck Model for Continuous Characters
data.nex NEXUS Data Example
chronopl Molecular Dating With Penalized Likelihood
gammaStat Gamma-Statistic of Pybus and Harvey
write.nexus.data Write Character Data In NEXUS Format
print.phylo Compact Display of a Phylogeny
correlogram.formula Phylogenetic Correlogram
landplants Gene Tree of 36 Landplant rbcL Sequences
vcv.phylo Phylogenetic Variance-covariance or Correlation Matrix
collapsed.intervals Collapsed Coalescent Intervals
mst Minimum Spanning Tree
theta.k Population Parameter THETA using Expected Number of Alleles
howmanytrees Calculate Numbers of Phylogenetic Trees
mlphylo Estimating Phylogenies by Maximum Likelihood
woodmouse Cytochrome b Gene Sequences of Woodmice
ladderize Ladderize a Tree
corClasses Phylogenetic Correlation Structures
skylineplot Drawing Skyline Plot Graphs
read.tree Read Tree File in Parenthetic Format
plot.phylo Plot Phylogenies
rotate Swopping sister clades
mantel.test Mantel Test for Similarity of Two Matrices
multi2di Collapse and Resolve Multichotomies
plot.varcomp Plot Variance Components
ratogram Ratogram Computed by Nonparametric Rate Smoothing
write.tree Write Tree File in Parenthetic Format
xenarthra Molecular Phylogeny of Living Xenarthrans
unique.multiPhylo Revomes Duplicate Trees
plot.ancestral Plot Ancestral Character Values on a Tree
read.GenBank Read DNA Sequences from GenBank via Internet
theta.s Population Parameter THETA using Segregating Sites in DNA Sequences
summary.phylo Print Summary of a Phylogeny
varcomp Compute Variance Component Estimates
yule.cov Fits the Yule Model With Covariates
nodelabels Labelling the Nodes, Tips, and Edges of a Tree
sh.test Shimodaira-Hasegawa Test
zoom Zoom on a Portion of a Phylogeny
which.edge Identifies Edges of a Tree
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