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ape (version 1.9-3)

Analyses of Phylogenetics and Evolution

Description

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 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 and ML methods.

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Version

Install

install.packages('ape')

Monthly Downloads

87,302

Version

1.9-3

License

GPL version 2 or newer

Maintainer

Emmanuel Paradis

Last Published

December 16th, 2024

Functions in ape (1.9-3)

as.phylo

Conversion Among Tree Objects
ltt.plot

Lineages Through Time Plot
klastorin

Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000)
diversi.time

Analysis of Diversification with Survival Models
birthdeath

Estimation of Speciation and Extinction Rates With Birth-Death Models
cherry

Number of Cherries and Null Models of Trees
add.scale.bar

Add a Scale Bar to a Phylogeny Plot
read.nexus

Read Tree File in Nexus Format
collapse.singles

Collapse Single Nodes
boot.phylo

Tree Bipartition and Bootstrapping Phylogenies
bird.families

Phylogeny of the Families of Birds From Sibley and Ahlquist
cophenetic.phylo

Pairwise Distances from a Phylogenetic Tree
base.freq

Base frequencies from DNA Sequences
nuc.div

Nucleotide Diversity
axisPhylo

Axis on Side of Phylogeny
corClasses

Phylogenetic Correlation Structures
mantel.test

Mantel Test for Similarity of Two Matrices
compar.ou

Ornstein--Uhlenbeck Model for Continuous Characters
consensus

Concensus Trees
balance

Balance of a Dichotomous Phylogenetic Tree
NPRS.criterion

Objective Function Employed in Nonparametric Rate Smoothing
data.nex

NEXUS Data Example
chronopl

Molecular Dating With Penalized Likelihood
mst

Minimum Spanning Tree
branching.times

Branching Times of a Phylogenetic Tree
diversi.gof

Tests of Constant Diversification Rates
plot.ancestral

Plot Ancestral Character Values on a Tree
as.matching

Conversion Between Phylo and Matching Objects
ladderize

Ladderize a Tree
howmanytrees

Calculate Numbers of Phylogenetic Trees
DNAmodel

Defines Models of DNA Evolution
all.equal.phylo

Global Comparison of two Phylogenies
gammaStat

Gamma-Statistic of Pybus and Harvey
Correlogram

Compute a correlogram
compar.lynch

Lynch's Comparative Method
discrete.dist

Taxonomic Level from a Pairwise Distances Matrix
heterozygosity

Heterozygosity at a Locus Using Gene Frequencies
plot.correlogram

Plot a Correlogram
is.ultrametric

Test if a Tree is Ultrametric
print.phylo

Compact Display of a Phylogeny
drop.tip

Remove Tips in a Phylogenetic Tree
read.GenBank

Read DNA Sequences from GenBank via Internet
root

Roots Phylogenetic Trees
nj

Neighbor-Joining Tree Estimation
theta.s

Population Parameter THETA using Segregating Sites in DNA Sequences
read.dna

Read DNA Sequences in a File
sh.test

Shimodaira-Hasegawa Test
weight.taxo

Pairwise Distances from a Taxonomic Level
nodelabels

Labelling the Nodes, Tips, and Edges of a Tree
compar.cheverud

Cheverud's Comparative Method
collapsed.intervals

Collapsed Coalescent Intervals
chronogram

Chronogram Computed by Nonparametric Rate Smoothing
seg.sites

Find Segregating Sites in DNA Sequences
summary.phylo

Print Summary of a Phylogeny
theta.h

Population Parameter THETA using Homozygosity
yule

Fits Yule Model to a Phylogenetic Tree
theta.k

Population Parameter THETA using Expected Number of Alleles
reorder.phylo

Internal Reordering of Trees
ratogram

Ratogram Computed by Nonparametric Rate Smoothing
node.depth

Depth of Nodes and Tips
Moran.I

Moran's I Autocorrelation Index
compute.brlen

Branch Lengths Computation
Initialize.corPhyl

Initialize a 'corPhyl' Structure Object
varcomp

Compute Variance Component Estimates
dist.gene

Pairwise Distances from Genetic Data
write.nexus

Write Tree File in Nexus Format
dist.dna

Pairwise Distances from DNA Sequences
phymltest

Fits a Bunch of Models with PHYML
GC.content

Content in GC from DNA Sequences
rtree

Generates Random Trees
bind.tree

Binds Trees
carnivora

Carnivora body sizes and life history traits
coalescent.intervals

Coalescent Intervals
multi2di

Collapse and Resolve Multichotomies
write.nexus.data

Write Character Data In NEXUS Format
compar.gee

Comparative Analysis with GEEs
bird.orders

Phylogeny of the Orders of Birds From Sibley and Ahlquist
opsin

Gene Tree of 32 opsin Sequences
read.caic

Read Tree File in CAIC Format
woodmouse

Cytochrome b Gene Sequences of Woodmice
mlphylo

Estimating Phylogenies by Maximum Likelihood
write.dna

Write DNA Sequences in a File
write.tree

Write Tree File in Parenthetic Format
which.edge

Identifies Edges of a Tree
xenarthra

Molecular Phylogeny of Living Xenarthrans
ace

Ancestral Character Estimation
chiroptera

Bat Phylogeny
as.phylo.formula

Conversion from Taxonomy Variables to Phylogenetic Trees
corBrownian

Brownian Correlation Structure
hivtree

Phylogenetic Tree of 193 HIV-1 Sequences
corGrafen

Grafen's (1989) Correlation Structure
mcmc.popsize

Reversible Jump MCMC to Infer Demographic History
pic

Phylogenetically Independent Contrasts
evolve.phylo

Ancestral Character Simulation
dist.topo

Topological Distances Between Two Trees
panel.superpose.correlogram

Lattice panel used in 'plot.correlogramList'.
ape-internal

Internal Ape Functions
mrca

Find Most Recent Common Ancestors Between Pairs
landplants

Gene Tree of 36 Landplant rbcL Sequences
plot.phylo

Plot Phylogenies
skyline

Skyline Plot Estimate of Effective Population Size
yule.cov

Fits the Yule Model With Covariates
bd.ext

Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
read.tree

Read Tree File in Parenthetic Format
plot.correlogramList

Plot several Correlograms
read.nexus.data

Read Character Data In NEXUS Format
vcv.phylo

Phylogenetic Variance-covariance or Correlation Matrix
zoom

Zoom on a Portion of a Phylogeny
skylineplot

Drawing Skyline Plot Graphs
plot.varcomp

Plot Variance Components
corMartins

Martins's (1997) Correlation Structure
is.binary.tree

Test for Binary Tree