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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, the population parameter theta based on various approaches, generalized skyline plots, estimation of absolute evolutionary rates and clock-like trees using non-parametric rate smoothing, conversion of APE trees to and from hclust objects and for classifying genes in trees using the Klastorin-Misawa-Tajima approach.

Functions in ape

Name Description
ratogram Ratogram Computed by Nonparametric Rate Smoothing
theta.h Population Parameter THETA using Homozygosity
ltt.plot Lineages Through Time Plot
bird.families Phylogeny of the Families of Birds From Sibley and Ahlquist
bird.orders Phylogeny of the Orders of Birds From Sibley and Ahlquist
hivtree Phylogenetic Tree of 193 HIV-1 Sequences
opsin Gene Tree of 32 opsin Sequences
read.dna Read DNA Sequences in a File
theta.k Population Parameter THETA using Expected Number of Alleles
coalescent.intervals Coalescent Intervals
chronogram Chronogram Computed by Nonparametric Rate Smoothing
cherry Number of Cherries and Null Models of Trees
diversi.time Analysis of Diversification with Survival Models
gamma.stat Gamma-Statistic of Pybus and Harvey
drop.tip Remove Tips in a Phylogenetic Tree
NPRS.criterion Objective Function Employed in Nonparametric Rate Smoothing
read.nexus Read Tree File in Nexus Format
ape-internal Internal Ape Functions
landplants Gene Tree of 36 Landplant rbcL Sequences
GC.content Content in GC from DNA Sequences
dist.dna Pairwise Distances from DNA Sequences
summary.phylo Print Summary of a Phylogeny
plot.phylo Plot Phylogenies
write.tree Write Tree File in Parenthetic Format
is.binary.tree Test for Binary Tree
branching.times Branching Times of a Phylogenetic Tree
diversi.gof Tests of Constant Diversification Rates
skylineplot Drawing Skyline Plot Graphs
theta.s Population Parameter THETA using Segregating Sites in DNA Sequences
base.freq Base frequencies from DNA Sequences
klastorin Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000)
collapsed.intervals Collapsed Coalescent Intervals
read.GenBank Read DNA Sequences from GenBank via Internet
mantel.test Mantel Test for Similarity of Two Matrices
woodmouse Cytochrome b Sequences of Woodmice
bind.tree Binds Trees
add.scale.bar Add a Scale Bar to a Phylogeny Plot
as.phylo Conversion between "phylo" and "hclust" trees
compar.lynch Lynch's Comparative Method
birthdeath Estimation of Speciation and Extinction Rates With Birth-Death Models
pic Phylogenetically Independent Contrasts
balance Balance of a Dichotomous Phylogenetic Tree
dist.gene Pairwise Distances from Genetic Data
is.ultrametric Test if a Tree is Ultrametric
heterozygosity Heterozygosity at a Locus Using Gene Frequencies
skyline Skyline Plot Estimate of Effective Population Size
dist.phylo Pairwise Distances from a Phylogenetic Tree
mst Minimum Spanning Tree
xenarthra Molecular Phylogeny of Living Xenarthrans
vcv.phylo Phylogenetic Variance-covariance or Correlation Matrix
all.equal.phylo Global Comparison of two Phylogenies
compar.gee Comparative Analysis with GEEs
write.dna Write DNA Sequences in a File
read.tree Read Tree File in Parenthetic Format
write.nexus Write Tree File in Nexus Format
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Date 2003-08-12
License GPL version 2 or newer
depends gee
Contributors Emmanuel Paradis

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