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

Date 2004-05-24
License GPL version 2 or newer
Packaged Mon May 24 00:31:49 2004; PARADYS
depends gee
Contributors Emmanuel Paradis

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