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ape (version 1.5)

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, conversion of APE trees to and from hclust objects and for classifying genes in trees using the Klastorin-Misawa-Tajima approach.

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Version

Install

install.packages('ape')

Monthly Downloads

84,031

Version

1.5

License

GPL version 2 or newer

Maintainer

Emmanuel Paradis

Last Published

December 16th, 2024

Functions in ape (1.5)

birthdeath

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

Calculate Numbers of Phylogenetic Trees
cherry

Number of Cherries and Null Models of Trees
read.GenBank

Read DNA Sequences from GenBank via Internet
GC.content

Content in GC from DNA Sequences
ape-internal

Internal Ape Functions
discrete.dist

Taxonomic Level from a Pairwise Distances Matrix
diversi.gof

Tests of Constant Diversification Rates
rtree

Generates Random Trees
drop.tip

Remove Tips in a Phylogenetic Tree
corGrafen

Grafen's (1989) Correlation Structure
as.matching

Conversion Between Phylo and Matching Objects
NPRS.criterion

Objective Function Employed in Nonparametric Rate Smoothing
Correlogram

Compute a correlogram
mst

Minimum Spanning Tree
bind.tree

Binds Trees
collapsed.intervals

Collapsed Coalescent Intervals
is.binary.tree

Test for Binary Tree
as.phylo

Conversion Among Tree Objects
all.equal.phylo

Global Comparison of two Phylogenies
balance

Balance of a Dichotomous Phylogenetic Tree
bd.ext

Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
base.freq

Base frequencies from DNA Sequences
phymltest

Fits a Bunch of Models with PHYML
compar.cheverud

Cheverud's Comparative Method
coalescent.intervals

Coalescent Intervals
corBrownian

Brownian Correlation Structure
read.dna

Read DNA Sequences in a File
axisPhylo

Axis on Side of Phylogeny
panel.superpose.correlogram

Lattice panel used in 'plot.correlogramList'.
read.tree

Read Tree File in Parenthetic Format
bird.families

Phylogeny of the Families of Birds From Sibley and Ahlquist
dist.gene

Pairwise Distances from Genetic Data
plot.varcomp

Plot Variance Components
heterozygosity

Heterozygosity at a Locus Using Gene Frequencies
landplants

Gene Tree of 36 Landplant rbcL Sequences
node.sons

Get the list of Sons for a Node
compar.gee

Comparative Analysis with GEEs
add.scale.bar

Add a Scale Bar to a Phylogeny Plot
ratogram

Ratogram Computed by Nonparametric Rate Smoothing
compar.lynch

Lynch's Comparative Method
ltt.plot

Lineages Through Time Plot
Moran.I

Moran's I Autocorrelation Index
corMartins

Martins's (1997) Correlation Structure
seg.sites

Find Segregating Sites in DNA Sequences
chiroptera

Bat Phylogeny
is.ultrametric

Test if a Tree is Ultrametric
skylineplot

Drawing Skyline Plot Graphs
Initialize.corPhyl

Initialize a 'corPhyl' Structure Object
write.dna

Write DNA Sequences in a File
diversi.time

Analysis of Diversification with Survival Models
theta.s

Population Parameter THETA using Segregating Sites in DNA Sequences
klastorin

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

Phylogeny of the Orders of Birds From Sibley and Ahlquist
branching.times

Branching Times of a Phylogenetic Tree
zoom

Zoom on a Portion of a Phylogeny
dist.taxo

Pairwise Distances from a Taxonomic Level
varcomp

Compute Variance Component Estimates
node.leafnumber

Get the Number of Leaves for a Node
compute.brlen

Branch lengths Computation
chronogram

Chronogram Computed by Nonparametric Rate Smoothing
carnivora

Carnivora body sizes and life history traits
nj

Neighbor-Joining Tree Estimation
skyline

Skyline Plot Estimate of Effective Population Size
vcv.phylo

Phylogenetic Variance-covariance or Correlation Matrix
opsin

Gene Tree of 32 opsin Sequences
corClasses

Phylogenetic Correlation Structures
mantel.test

Mantel Test for Similarity of Two Matrices
mcmc.popsize

Reversible Jump MCMC to Infer Demographic History
dist.dna

Pairwise Distances from DNA Sequences
which.edge

Identifies Edges of a Tree
write.tree

Write Tree File in Parenthetic Format
node.depth

Depth of Nodes and Tips
xenarthra

Molecular Phylogeny of Living Xenarthrans
multi2di

Collapse and Resolve Multichotomies
pic

Phylogenetically Independent Contrasts
dist.phylo

Pairwise Distances from a Phylogenetic Tree
gammaStat

Gamma-Statistic of Pybus and Harvey
theta.h

Population Parameter THETA using Homozygosity
rotate

Rotate an Internal Branch of a Tree
root

Roots Phylogenetic Trees
plot.phylo

Plot Phylogenies
woodmouse

Cytochrome b Gene Sequences of Woodmice
read.nexus

Read Tree File in Nexus Format
theta.k

Population Parameter THETA using Expected Number of Alleles
nuc.div

Nucleotide Diversity
plot.correlogramList

Plot several Correlograms
hivtree

Phylogenetic Tree of 193 HIV-1 Sequences
nodelabels

Labelling the Nodes of a Tree
summary.phylo

Print Summary of a Phylogeny
plot.correlogram

Plot a Correlogram
write.nexus

Write Tree File in Nexus Format
yule.cov

Fits the Yule Model With Covariates
yule

Fits Yule Model to a Phylogenetic Tree