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ape (version 1.9-1)

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

1.9-1

License

GPL version 2 or newer

Maintainer

Emmanuel Paradis

Last Published

December 16th, 2024

Functions in ape (1.9-1)

branching.times

Branching Times of a Phylogenetic Tree
dist.gene

Pairwise Distances from Genetic Data
dist.topo

Topological Distances Between Two Trees
howmanytrees

Calculate Numbers of Phylogenetic Trees
collapse.singles

Collapse Single Nodes
carnivora

Carnivora body sizes and life history traits
plot.ancestral

Plot Ancestral Character Values on a Tree
compute.brlen

Branch Lengths Computation
nj

Neighbor-Joining Tree Estimation
axisPhylo

Axis on Side of Phylogeny
balance

Balance of a Dichotomous Phylogenetic Tree
all.equal.phylo

Global Comparison of two Phylogenies
compar.cheverud

Cheverud's Comparative Method
seg.sites

Find Segregating Sites in DNA Sequences
Correlogram

Compute a correlogram
collapsed.intervals

Collapsed Coalescent Intervals
diversi.gof

Tests of Constant Diversification Rates
pic

Phylogenetically Independent Contrasts
print.phylo

Compact Display of a Phylogeny
bird.orders

Phylogeny of the Orders of Birds From Sibley and Ahlquist
NPRS.criterion

Objective Function Employed in Nonparametric Rate Smoothing
diversi.time

Analysis of Diversification with Survival Models
consensus

Concensus Trees
ltt.plot

Lineages Through Time Plot
hivtree

Phylogenetic Tree of 193 HIV-1 Sequences
xenarthra

Molecular Phylogeny of Living Xenarthrans
rotate

Rotate an Internal Branch of a Tree
Moran.I

Moran's I Autocorrelation Index
ace

Ancestral Character Estimation
plot.correlogram

Plot a Correlogram
read.nexus.data

Read Character Data In NEXUS Format
landplants

Gene Tree of 36 Landplant rbcL Sequences
as.phylo

Conversion Among Tree Objects
Initialize.corPhyl

Initialize a 'corPhyl' Structure Object
coalescent.intervals

Coalescent Intervals
bind.tree

Binds Trees
read.dna

Read DNA Sequences in a File
ape-internal

Internal Ape Functions
rtree

Generates Random Trees
bd.ext

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

Read Tree File in Nexus Format
nuc.div

Nucleotide Diversity
corMartins

Martins's (1997) Correlation Structure
varcomp

Compute Variance Component Estimates
reorder.phylo

Internal Reordering of Trees
compar.ou

Ornstein--Uhlenbeck Model for Continuous Characters
read.GenBank

Read DNA Sequences from GenBank via Internet
plot.varcomp

Plot Variance Components
chiroptera

Bat Phylogeny
heterozygosity

Heterozygosity at a Locus Using Gene Frequencies
corBrownian

Brownian Correlation Structure
klastorin

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

Depth of Nodes and Tips
zoom

Zoom on a Portion of a Phylogeny
compar.gee

Comparative Analysis with GEEs
cophenetic.phylo

Pairwise Distances from a Phylogenetic Tree
skyline

Skyline Plot Estimate of Effective Population Size
corClasses

Phylogenetic Correlation Structures
yule

Fits Yule Model to a Phylogenetic Tree
write.dna

Write DNA Sequences in a File
mrca

Find Most Recent Common Ancestors Between Pairs
which.edge

Identifies Edges of a Tree
skylineplot

Drawing Skyline Plot Graphs
dist.dna

Pairwise Distances from DNA Sequences
data.nex

NEXUS Data Example
as.phylo.formula

Conversion from Taxonomy Variables to Phylogenetic Trees
drop.tip

Remove Tips in a Phylogenetic Tree
read.tree

Read Tree File in Parenthetic Format
woodmouse

Cytochrome b Gene Sequences of Woodmice
plot.phylo

Plot Phylogenies
write.nexus

Write Tree File in Nexus Format
boot.phylo

Tree Bipartition and Bootstrapping Phylogenies
summary.phylo

Print Summary of a Phylogeny
is.ultrametric

Test if a Tree is Ultrametric
mst

Minimum Spanning Tree
mcmc.popsize

Reversible Jump MCMC to Infer Demographic History
mantel.test

Mantel Test for Similarity of Two Matrices
theta.s

Population Parameter THETA using Segregating Sites in DNA Sequences
gammaStat

Gamma-Statistic of Pybus and Harvey
is.binary.tree

Test for Binary Tree
panel.superpose.correlogram

Lattice panel used in 'plot.correlogramList'.
multi2di

Collapse and Resolve Multichotomies
evolve.phylo

Ancestral Character Simulation
weight.taxo

Pairwise Distances from a Taxonomic Level
root

Roots Phylogenetic Trees
ratogram

Ratogram Computed by Nonparametric Rate Smoothing
theta.h

Population Parameter THETA using Homozygosity
yule.cov

Fits the Yule Model With Covariates
write.tree

Write Tree File in Parenthetic Format
nodelabels

Labelling the Nodes and the Tips of a Tree
GC.content

Content in GC from DNA Sequences
DNAmodel

Defines Models of DNA Evolution
mlphylo

Estimating Phylogenies by Maximum Likelihood
theta.k

Population Parameter THETA using Expected Number of Alleles
corGrafen

Grafen's (1989) Correlation Structure
base.freq

Base frequencies from DNA Sequences
chronogram

Chronogram Computed by Nonparametric Rate Smoothing
compar.lynch

Lynch's Comparative Method
plot.correlogramList

Plot several Correlograms
sh.test

Shimodaira-Hasegawa Test
add.scale.bar

Add a Scale Bar to a Phylogeny Plot
chronopl

Molecular Dating With Penalized Likelihood
phymltest

Fits a Bunch of Models with PHYML
cherry

Number of Cherries and Null Models of Trees
bird.families

Phylogeny of the Families of Birds From Sibley and Ahlquist
read.caic

Read Tree File in CAIC Format
as.matching

Conversion Between Phylo and Matching Objects
birthdeath

Estimation of Speciation and Extinction Rates With Birth-Death Models
discrete.dist

Taxonomic Level from a Pairwise Distances Matrix
opsin

Gene Tree of 32 opsin Sequences
write.nexus.data

Write Character Data In NEXUS Format
vcv.phylo

Phylogenetic Variance-covariance or Correlation Matrix
ladderize

Ladderize a Tree