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ape (version 0.2-1)

Analyses of Phylogenetics and Evolution

Description

Ape provides functions for reading, writing, and plotting phylogenetic trees in parenthetic format (standard Newick format), analyses of comparative data in a phylogenetic framework, analyses of diversification and macroevolution, computing distances from allelic and nucleotide data, reading nucleotide sequences from GenBank via internet, 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

0.2-1

License

GPL version 2 or newer

Maintainer

Emmanuel Paradis

Last Published

December 16th, 2024

Functions in ape (0.2-1)

balance

Balance of a Dichotomous Phylogenetic Tree
base.freq

Base frequencies from DNA Sequences
compar.lynch

Lynch's Comparative Method
branching.times

Branching Times of a Phylogenetic Tree
ltt.plot

Lineages Through Time Plot
read.GenBank

Read DNA Sequences from GenBank via Internet
theta.s

Population Parameter THETA using Segregating Sites in DNA Sequences
pic

Phylogenetically Independent Contrasts
cherry

Number of Cherries and Null Models of Trees
read.tree

Read Tree File in Parenthetic Format
heterozygosity

Heterozygosity at a Locus Using Gene Frequencies
dist.phylo

Pairwise Distances from a Phylogenetic Tree
birthdeath

Estimation of Speciation and Extinction Rates With Birth-Death Models
theta.h

Population Parameter THETA using Homozygosity
vcv.phylo

Phylogenetic Variance-covariance or Correlation Matrix
plot.phylo

Plot Phylogenies
bird.families

Phylogeny of the Families of Birds From Sibley and Ahlquist
GC.content

Content in GC from DNA Sequences
ape-internal

Internal Ape Functions
is.binary.tree

Test for Binary Tree
coalescent.intervals

Coalescent Intervals
mst

Minimum Spanning Tree
theta.k

Population Parameter THETA using Expected Number of Alleles
hivtree

Phylogenetic Tree of 193 HIV-1 Sequences
collapsed.intervals

Collapsed Coalescent Intervals
mantel.test

Mantel Test for Similarity of Two Matrices
dist.gene

Pairwise Distances from Genetic Data
write.tree

Write Tree File in Parenthetic Format
diversi.gof

Tests of Constant Diversification Rates
dist.dna

Pairwise Distances from DNA Sequences
diversi.time

Analysis of Diversification with Survival Models
add.scale.bar

Add a Scale Bar to a Phylogeny Plot
gamma.stat

Gamma-Statistic of Pybus and Harvey
skylineplot

Drawing Skyline Plot Graphs
compar.gee

Comparative Analysis with GEEs
all.equal.phylo

Global Comparison of two Phylogenies
skyline

Skyline Plot Estimate of Effective Population Size