ape v0.1

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Analyses of Phylogenetics and Evolution

Ape provides functions for reading, 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
diversi.time Analysis of Diversification with Survival Models
vcv.phylo Phylogenetic Variance-covariance or Correlation Matrix
GC.content Content in GC from DNA Sequences
compar.lynch Lynch's Comparative Method
dist.gene Pairwise Distances from Genetic Data
dist.dna Pairwise Distances from DNA Sequences
ape-internal Internal Ape Functions
all.equal.phylo Global Comparison of two Phylogenies
compar.gee Comparative Analysis with GEEs
mantel.test Mantel Test for Similarity of Two Matrices
theta.s Population Parameter THETA using Segregating Sites in DNA Sequences
balance Balance of a Dichotomous Phylogenetic Tree
theta.k Population Parameter THETA using Expected Number of Alleles
pic Phylogenetically Independent Contrasts
cherry Number of Cherries and Null Models of Trees
read.tree Read Tree File in Parenthetic Format
skyline.plot Skyline Plot of Estimated Effective Population Size
heterozygosity Heterozygosity at a Locus Using Gene Frequencies
diversi.gof Tests of Constant Diversification Rates
gamma.stat Gamma-Statistic of Pybus and Harvey
branching.times Branching Times of a Phylogenetic Tree
base.freq Base frequencies from DNA Sequences
theta.h Population Parameter THETA using Homozigosity
ltt.plot Lineages Through Time Plot
plot.phylo Plot Phylogenies
read.GenBank Read DNA Sequences from GenBank via Internet
dist.phylo Pairwise Distances from a Phylogenetic Tree
mst Minimum Spanning Tree
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Date 2002-08-27
License GPL version 2 or newer

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