ape v2.1-1


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