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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
carnivora Carnivora body sizes and life history traits
bird.orders Phylogeny of the Orders of Birds From Sibley and Ahlquist
gammaStat Gamma-Statistic of Pybus and Harvey
is.binary.tree Test for Binary Tree
read.GenBank Read DNA Sequences from GenBank via Internet
plot.correlogram Plot a Correlogram
opsin Gene Tree of 32 opsin Sequences
bind.tree Binds Trees
coalescent.intervals Coalescent Intervals
mantel.test Mantel Test for Similarity of Two Matrices
diversi.gof Tests of Constant Diversification Rates
NPRS.criterion Objective Function Employed in Nonparametric Rate Smoothing
branching.times Branching Times of a Phylogenetic Tree
chronogram Chronogram Computed by Nonparametric Rate Smoothing
summary.phylo Print Summary of a Phylogeny
seg.sites Find Segregating Sites in DNA Sequences
cherry Number of Cherries and Null Models of Trees
node.depth Depth of Nodes and Tips
dist.gene Pairwise Distances from Genetic Data
landplants Gene Tree of 36 Landplant rbcL Sequences
theta.s Population Parameter THETA using Segregating Sites in DNA Sequences
ape-internal Internal Ape Functions
collapsed.intervals Collapsed Coalescent Intervals
dist.taxo Pairwise Distances from a Taxonomic Level
pic Phylogenetically Independent Contrasts
zoom Zoom on a Portion of a Phylogeny
is.ultrametric Test if a Tree is Ultrametric
bird.families Phylogeny of the Families of Birds From Sibley and Ahlquist
theta.h Population Parameter THETA using Homozygosity
Moran.I Moran's I Autocorrelation Index
as.phylo Conversion between "phylo" and "hclust" trees
drop.tip Remove Tips in a Phylogenetic Tree
chiroptera Bat Phylogeny
compar.gee Comparative Analysis with GEEs
write.nexus Write Tree File in Nexus Format
diversi.time Analysis of Diversification with Survival Models
node.depth.edgelength Distance from Root to Nodes and Tips
dist.dna Pairwise Distances from DNA Sequences
skylineplot Drawing Skyline Plot Graphs
read.tree Read Tree File in Parenthetic Format
hivtree Phylogenetic Tree of 193 HIV-1 Sequences
woodmouse Cytochrome b Sequences of Woodmice
ltt.plot Lineages Through Time Plot
mst Minimum Spanning Tree
ratogram Ratogram Computed by Nonparametric Rate Smoothing
read.nexus Read Tree File in Nexus Format
read.dna Read DNA Sequences in a File
yule Fits Yule Model to a Phylogenetic Tree
plot.phylo Plot Phylogenies
theta.k Population Parameter THETA using Expected Number of Alleles
vcv.phylo Phylogenetic Variance-covariance or Correlation Matrix
dist.phylo Pairwise Distances from a Phylogenetic Tree
base.freq Base frequencies from DNA Sequences
skyline Skyline Plot Estimate of Effective Population Size
write.dna Write DNA Sequences in a File
add.scale.bar Add a Scale Bar to a Phylogeny Plot
bd.ext Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
balance Balance of a Dichotomous Phylogenetic Tree
birthdeath Estimation of Speciation and Extinction Rates With Birth-Death Models
GC.content Content in GC from DNA Sequences
all.equal.phylo Global Comparison of two Phylogenies
Correlogram Compute a correlogram
heterozygosity Heterozygosity at a Locus Using Gene Frequencies
rtree Generates Random Trees
xenarthra Molecular Phylogeny of Living Xenarthrans
write.tree Write Tree File in Parenthetic Format
klastorin Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000)
popsize Reversible Jump MCMC to Infer Demographic History
compar.lynch Lynch's Comparative Method
discrete.dist Taxonomic Level from a Pairwise Distances Matrix
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Date 2004-09-16
License GPL version 2 or newer
Packaged Thu Sep 16 21:39:46 2004; PARADYS
suggests gee
Contributors Emmanuel Paradis

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