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ape (version 1.0)

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, or the population parameter theta based on various approaches.

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Version

Install

install.packages('ape')

Monthly Downloads

87,302

Version

1.0

License

GPL version 2 or newer

Maintainer

Emmanuel Paradis

Last Published

December 16th, 2024

Functions in ape (1.0)

bird.orders

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

Lynch's Comparative Method
branching.times

Branching Times of a Phylogenetic Tree
pic

Phylogenetically Independent Contrasts
theta.h

Population Parameter THETA using Homozygosity
ape-internal

Internal Ape Functions
dist.phylo

Pairwise Distances from a Phylogenetic Tree
diversi.gof

Tests of Constant Diversification Rates
ltt.plot

Lineages Through Time Plot
base.freq

Base frequencies from DNA Sequences
write.dna

Write DNA Sequences in a File
mantel.test

Mantel Test for Similarity of Two Matrices
read.nexus

Read Tree File in Nexus Format
skylineplot

Drawing Skyline Plot Graphs
compar.gee

Comparative Analysis with GEEs
gamma.stat

Gamma-Statistic of Pybus and Harvey
add.scale.bar

Add a Scale Bar to a Phylogeny Plot
dist.dna

Pairwise Distances from DNA Sequences
read.tree

Read Tree File in Parenthetic Format
theta.k

Population Parameter THETA using Expected Number of Alleles
bird.families

Phylogeny of the Families of Birds From Sibley and Ahlquist
mst

Minimum Spanning Tree
balance

Balance of a Dichotomous Phylogenetic Tree
is.binary.tree

Test for Binary Tree
dist.gene

Pairwise Distances from Genetic Data
GC.content

Content in GC from DNA Sequences
heterozygosity

Heterozygosity at a Locus Using Gene Frequencies
write.tree

Write Tree File in Parenthetic Format
is.ultrametric

Test if a Tree is Ultrametric
read.dna

Read DNA Sequences in a File
drop.tip

Remove Tips in a Phylogenetic Tree
write.nexus

Write Tree File in Nexus Format
skyline

Skyline Plot Estimate of Effective Population Size
diversi.time

Analysis of Diversification with Survival Models
cherry

Number of Cherries and Null Models of Trees
hivtree

Phylogenetic Tree of 193 HIV-1 Sequences
read.GenBank

Read DNA Sequences from GenBank via Internet
collapsed.intervals

Collapsed Coalescent Intervals
coalescent.intervals

Coalescent Intervals
birthdeath

Estimation of Speciation and Extinction Rates With Birth-Death Models
bind.tree

Binds Trees
vcv.phylo

Phylogenetic Variance-covariance or Correlation Matrix
plot.phylo

Plot Phylogenies
theta.s

Population Parameter THETA using Segregating Sites in DNA Sequences
all.equal.phylo

Global Comparison of two Phylogenies