ape v1.2-7


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


Date 2004-09-23
ZipData no
License GPL version 2 or newer
Packaged Fri Sep 24 09:49:28 2004; PARADYS

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