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ape (version 1.1-2)

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, 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

1.1-2

License

GPL version 2 or newer

Maintainer

Emmanuel Paradis

Last Published

December 16th, 2024

Functions in ape (1.1-2)

add.scale.bar

Add a Scale Bar to a Phylogeny Plot
coalescent.intervals

Coalescent Intervals
all.equal.phylo

Global Comparison of two Phylogenies
heterozygosity

Heterozygosity at a Locus Using Gene Frequencies
theta.s

Population Parameter THETA using Segregating Sites in DNA Sequences
compar.gee

Comparative Analysis with GEEs
hivtree

Phylogenetic Tree of 193 HIV-1 Sequences
compar.lynch

Lynch's Comparative Method
ltt.plot

Lineages Through Time Plot
plot.phylo

Plot Phylogenies
summary.phylo

Print Summary of a Phylogeny
klastorin

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

Objective Function Employed in Nonparametric Rate Smoothing
diversi.time

Analysis of Diversification with Survival Models
read.dna

Read DNA Sequences in a File
cherry

Number of Cherries and Null Models of Trees
read.tree

Read Tree File in Parenthetic Format
vcv.phylo

Phylogenetic Variance-covariance or Correlation Matrix
chronogram

Chronogram Computed by Nonparametric Rate Smoothing
bind.tree

Binds Trees
ape-internal

Internal Ape Functions
opsin

Gene Tree of 32 opsin Sequences
landplants

Gene Tree of 36 Landplant rbcL Sequences
drop.tip

Remove Tips in a Phylogenetic Tree
theta.k

Population Parameter THETA using Expected Number of Alleles
write.dna

Write DNA Sequences in a File
write.nexus

Write Tree File in Nexus Format
woodmouse

Cytochrome b Sequences of Woodmice
theta.h

Population Parameter THETA using Homozygosity
is.ultrametric

Test if a Tree is Ultrametric
bird.orders

Phylogeny of the Orders of Birds From Sibley and Ahlquist
mantel.test

Mantel Test for Similarity of Two Matrices
birthdeath

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

Pairwise Distances from Genetic Data
gamma.stat

Gamma-Statistic of Pybus and Harvey
diversi.gof

Tests of Constant Diversification Rates
GC.content

Content in GC from DNA Sequences
read.nexus

Read Tree File in Nexus Format
skylineplot

Drawing Skyline Plot Graphs
ratogram

Ratogram Computed by Nonparametric Rate Smoothing
dist.dna

Pairwise Distances from DNA Sequences
write.tree

Write Tree File in Parenthetic Format
base.freq

Base frequencies from DNA Sequences
balance

Balance of a Dichotomous Phylogenetic Tree
as.phylo

Conversion between "phylo" and "hclust" trees
collapsed.intervals

Collapsed Coalescent Intervals
bird.families

Phylogeny of the Families of Birds From Sibley and Ahlquist
skyline

Skyline Plot Estimate of Effective Population Size
branching.times

Branching Times of a Phylogenetic Tree
pic

Phylogenetically Independent Contrasts
dist.phylo

Pairwise Distances from a Phylogenetic Tree
mst

Minimum Spanning Tree
xenarthra

Molecular Phylogeny of Living Xenarthrans
read.GenBank

Read DNA Sequences from GenBank via Internet
is.binary.tree

Test for Binary Tree