ape v2.2-1


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