ape v2.3-2

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