ape v2.2-4

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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, and ME methods.

Functions in ape

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