Learn R Programming

⚠️There's a newer version (5.8-1) of this package.Take me there.

ape (version 1.10-2)

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.

Copy Link

Version

Install

install.packages('ape')

Monthly Downloads

84,031

Version

1.10-2

License

GPL version 2 or newer

Maintainer

Emmanuel Paradis

Last Published

December 16th, 2024

Functions in ape (1.10-2)

gammaStat

Gamma-Statistic of Pybus and Harvey
mcmc.popsize

Reversible Jump MCMC to Infer Demographic History
heterozygosity

Heterozygosity at a Locus Using Gene Frequencies
drop.tip

Remove Tips in a Phylogenetic Tree
base.freq

Base frequencies from DNA Sequences
bind.tree

Binds Trees
Moran.I

Moran's I Autocorrelation Index
axisPhylo

Axis on Side of Phylogeny
DNAbin

Manipulate DNA Sequences in Bit-Level Format
compute.brlen

Branch Lengths Computation
Initialize.corPhyl

Initialize a 'corPhyl' Structure Object
bird.families

Phylogeny of the Families of Birds From Sibley and Ahlquist
DNAmodel

Defines Models of DNA Evolution
as.matching

Conversion Between Phylo and Matching Objects
collapse.singles

Collapse Single Nodes
corBrownian

Brownian Correlation Structure
as.alignment

Conversion Among DNA Sequence Internal Formats
ace

Ancestral Character Estimation
coalescent.intervals

Coalescent Intervals
boot.phylo

Tree Bipartition and Bootstrapping Phylogenies
GC.content

Content in GC from DNA Sequences
dist.dna

Pairwise Distances from DNA Sequences
corClasses

Phylogenetic Correlation Structures
howmanytrees

Calculate Numbers of Phylogenetic Trees
as.phylo.formula

Conversion from Taxonomy Variables to Phylogenetic Trees
all.equal.phylo

Global Comparison of two Phylogenies
birthdeath

Estimation of Speciation and Extinction Rates With Birth-Death Models
bd.ext

Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
carnivora

Carnivora body sizes and life history traits
bird.orders

Phylogeny of the Orders of Birds From Sibley and Ahlquist
compar.gee

Comparative Analysis with GEEs
plot.ancestral

Plot Ancestral Character Values on a Tree
as.phylo

Conversion Among Tree Objects
consensus

Concensus Trees
chronopl

Molecular Dating With Penalized Likelihood
evolve.phylo

Ancestral Character Simulation
Correlogram

Compute a correlogram
skylineplot

Drawing Skyline Plot Graphs
add.scale.bar

Add a Scale Bar to a Phylogeny Plot
cherry

Number of Cherries and Null Models of Trees
is.binary.tree

Test for Binary Tree
NPRS.criterion

Objective Function Employed in Nonparametric Rate Smoothing
data.nex

NEXUS Data Example
branching.times

Branching Times of a Phylogenetic Tree
compar.cheverud

Cheverud's Comparative Method
corMartins

Martins's (1997) Correlation Structure
dist.gene

Pairwise Distances from Genetic Data
plot.correlogramList

Plot several Correlograms
cophenetic.phylo

Pairwise Distances from a Phylogenetic Tree
balance

Balance of a Dichotomous Phylogenetic Tree
mantel.test

Mantel Test for Similarity of Two Matrices
plot.correlogram

Plot a Correlogram
read.caic

Read Tree File in CAIC Format
discrete.dist

Taxonomic Level from a Pairwise Distances Matrix
compar.lynch

Lynch's Comparative Method
ltt.plot

Lineages Through Time Plot
vcv.phylo

Phylogenetic Variance-covariance or Correlation Matrix
ape-internal

Internal Ape Functions
xenarthra

Molecular Phylogeny of Living Xenarthrans
theta.k

Population Parameter THETA using Expected Number of Alleles
is.ultrametric

Test if a Tree is Ultrametric
multi2di

Collapse and Resolve Multichotomies
chiroptera

Bat Phylogeny
compar.ou

Ornstein--Uhlenbeck Model for Continuous Characters
read.nexus

Read Tree File in Nexus Format
dist.topo

Topological Distances Between Two Trees
ladderize

Ladderize a Tree
mlphylo

Estimating Phylogenies by Maximum Likelihood
print.phylo

Compact Display of a Phylogeny
read.GenBank

Read DNA Sequences from GenBank via Internet
collapsed.intervals

Collapsed Coalescent Intervals
theta.h

Population Parameter THETA using Homozygosity
hivtree

Phylogenetic Tree of 193 HIV-1 Sequences
nodelabels

Labelling the Nodes, Tips, and Edges of a Tree
root

Roots Phylogenetic Trees
landplants

Gene Tree of 36 Landplant rbcL Sequences
read.tree

Read Tree File in Parenthetic Format
chronogram

Chronogram Computed by Nonparametric Rate Smoothing
mst

Minimum Spanning Tree
summary.phylo

Print Summary of a Phylogeny
rtree

Generates Random Trees
corGrafen

Grafen's (1989) Correlation Structure
read.nexus.data

Read Character Data In NEXUS Format
weight.taxo

Pairwise Distances from a Taxonomic Level
nj

Neighbor-Joining Tree Estimation
seg.sites

Find Segregating Sites in DNA Sequences
nuc.div

Nucleotide Diversity
diversi.gof

Tests of Constant Diversification Rates
klastorin

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

Fits a Bunch of Models with PHYML
theta.s

Population Parameter THETA using Segregating Sites in DNA Sequences
panel.superpose.correlogram

Lattice panel used in 'plot.correlogramList'.
yule

Fits Yule Model to a Phylogenetic Tree
read.dna

Read DNA Sequences in a File
mrca

Find Most Recent Common Ancestors Between Pairs
diversi.time

Analysis of Diversification with Survival Models
which.edge

Identifies Edges of a Tree
pic

Phylogenetically Independent Contrasts
write.tree

Write Tree File in Parenthetic Format
skyline

Skyline Plot Estimate of Effective Population Size
opsin

Gene Tree of 32 opsin Sequences
write.nexus.data

Write Character Data In NEXUS Format
yule.cov

Fits the Yule Model With Covariates
reorder.phylo

Internal Reordering of Trees
write.nexus

Write Tree File in Nexus Format
node.depth

Depth of Nodes and Tips
sh.test

Shimodaira-Hasegawa Test
plot.varcomp

Plot Variance Components
ratogram

Ratogram Computed by Nonparametric Rate Smoothing
woodmouse

Cytochrome b Gene Sequences of Woodmice
varcomp

Compute Variance Component Estimates
plot.phylo

Plot Phylogenies
write.dna

Write DNA Sequences in a File
zoom

Zoom on a Portion of a Phylogeny