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ape (version 1.2-3)

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, 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

87,302

Version

1.2-3

License

GPL version 2 or newer

Maintainer

Emmanuel Paradis

Last Published

December 16th, 2024

Functions in ape (1.2-3)

GC.content

Content in GC from DNA Sequences
balance

Balance of a Dichotomous Phylogenetic Tree
NPRS.criterion

Objective Function Employed in Nonparametric Rate Smoothing
cherry

Number of Cherries and Null Models of Trees
bind.tree

Binds Trees
dist.phylo

Pairwise Distances from a Phylogenetic Tree
bird.orders

Phylogeny of the Orders of Birds From Sibley and Ahlquist
plot.phylo

Plot Phylogenies
heterozygosity

Heterozygosity at a Locus Using Gene Frequencies
compar.lynch

Lynch's Comparative Method
mst

Minimum Spanning Tree
opsin

Gene Tree of 32 opsin Sequences
ape-internal

Internal Ape Functions
mantel.test

Mantel Test for Similarity of Two Matrices
node.depth.edgelength

Distance from Root to Nodes and Tips
hivtree

Phylogenetic Tree of 193 HIV-1 Sequences
drop.tip

Remove Tips in a Phylogenetic Tree
coalescent.intervals

Coalescent Intervals
diversi.gof

Tests of Constant Diversification Rates
is.binary.tree

Test for Binary Tree
gammaStat

Gamma-Statistic of Pybus and Harvey
klastorin

Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000)
all.equal.phylo

Global Comparison of two Phylogenies
dist.dna

Pairwise Distances from DNA Sequences
node.depth

Depth of Nodes and Tips
chiroptera

Bat Phylogeny
as.phylo

Conversion between "phylo" and "hclust" trees
skyline

Skyline Plot Estimate of Effective Population Size
chronogram

Chronogram Computed by Nonparametric Rate Smoothing
read.dna

Read DNA Sequences in a File
dist.gene

Pairwise Distances from Genetic Data
branching.times

Branching Times of a Phylogenetic Tree
base.freq

Base frequencies from DNA Sequences
xenarthra

Molecular Phylogeny of Living Xenarthrans
summary.phylo

Print Summary of a Phylogeny
zoom

Zoom on a Portion of a Phylogeny
theta.s

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

Read Tree File in Nexus Format
theta.h

Population Parameter THETA using Homozygosity
write.tree

Write Tree File in Parenthetic Format
add.scale.bar

Add a Scale Bar to a Phylogeny Plot
seg.sites

Find Segregating Sites in DNA Sequences
birthdeath

Estimation of Speciation and Extinction Rates With Birth-Death Models
ltt.plot

Lineages Through Time Plot
is.ultrametric

Test if a Tree is Ultrametric
pic

Phylogenetically Independent Contrasts
compar.gee

Comparative Analysis with GEEs
bird.families

Phylogeny of the Families of Birds From Sibley and Ahlquist
write.dna

Write DNA Sequences in a File
skylineplot

Drawing Skyline Plot Graphs
read.GenBank

Read DNA Sequences from GenBank via Internet
vcv.phylo

Phylogenetic Variance-covariance or Correlation Matrix
yule

Fits Yule Model to a Phylogenetic Tree
landplants

Gene Tree of 36 Landplant rbcL Sequences
read.tree

Read Tree File in Parenthetic Format
theta.k

Population Parameter THETA using Expected Number of Alleles
ratogram

Ratogram Computed by Nonparametric Rate Smoothing
collapsed.intervals

Collapsed Coalescent Intervals
woodmouse

Cytochrome b Sequences of Woodmice
write.nexus

Write Tree File in Nexus Format
diversi.time

Analysis of Diversification with Survival Models
rtree

Generates Random Trees