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Analyses of Phylogenetics and Evolution

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.

Functions in ape

Name Description
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
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Details

Date 2003-2-23
License GPL version 2 or newer
depends gee
Contributors Emmanuel Paradis

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