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Analyses of Phylogenetics and Evolution

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.

Functions in ape

Name Description
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
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Date 2002-10-28
License GPL version 2 or newer

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