ape v1.5

0

Monthly downloads

0th

Percentile

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, nucleotide diversity, 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
birthdeath Estimation of Speciation and Extinction Rates With Birth-Death Models
howmanytrees Calculate Numbers of Phylogenetic Trees
cherry Number of Cherries and Null Models of Trees
read.GenBank Read DNA Sequences from GenBank via Internet
GC.content Content in GC from DNA Sequences
ape-internal Internal Ape Functions
discrete.dist Taxonomic Level from a Pairwise Distances Matrix
diversi.gof Tests of Constant Diversification Rates
rtree Generates Random Trees
drop.tip Remove Tips in a Phylogenetic Tree
corGrafen Grafen's (1989) Correlation Structure
as.matching Conversion Between Phylo and Matching Objects
NPRS.criterion Objective Function Employed in Nonparametric Rate Smoothing
Correlogram Compute a correlogram
mst Minimum Spanning Tree
bind.tree Binds Trees
collapsed.intervals Collapsed Coalescent Intervals
is.binary.tree Test for Binary Tree
as.phylo Conversion Among Tree Objects
all.equal.phylo Global Comparison of two Phylogenies
balance Balance of a Dichotomous Phylogenetic Tree
bd.ext Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
base.freq Base frequencies from DNA Sequences
phymltest Fits a Bunch of Models with PHYML
compar.cheverud Cheverud's Comparative Method
coalescent.intervals Coalescent Intervals
corBrownian Brownian Correlation Structure
read.dna Read DNA Sequences in a File
axisPhylo Axis on Side of Phylogeny
panel.superpose.correlogram Lattice panel used in 'plot.correlogramList'.
read.tree Read Tree File in Parenthetic Format
bird.families Phylogeny of the Families of Birds From Sibley and Ahlquist
dist.gene Pairwise Distances from Genetic Data
plot.varcomp Plot Variance Components
heterozygosity Heterozygosity at a Locus Using Gene Frequencies
landplants Gene Tree of 36 Landplant rbcL Sequences
node.sons Get the list of Sons for a Node
compar.gee Comparative Analysis with GEEs
add.scale.bar Add a Scale Bar to a Phylogeny Plot
ratogram Ratogram Computed by Nonparametric Rate Smoothing
compar.lynch Lynch's Comparative Method
ltt.plot Lineages Through Time Plot
Moran.I Moran's I Autocorrelation Index
corMartins Martins's (1997) Correlation Structure
seg.sites Find Segregating Sites in DNA Sequences
chiroptera Bat Phylogeny
is.ultrametric Test if a Tree is Ultrametric
skylineplot Drawing Skyline Plot Graphs
Initialize.corPhyl Initialize a 'corPhyl' Structure Object
write.dna Write DNA Sequences in a File
diversi.time Analysis of Diversification with Survival Models
theta.s Population Parameter THETA using Segregating Sites in DNA Sequences
klastorin Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000)
bird.orders Phylogeny of the Orders of Birds From Sibley and Ahlquist
branching.times Branching Times of a Phylogenetic Tree
zoom Zoom on a Portion of a Phylogeny
dist.taxo Pairwise Distances from a Taxonomic Level
varcomp Compute Variance Component Estimates
node.leafnumber Get the Number of Leaves for a Node
compute.brlen Branch lengths Computation
chronogram Chronogram Computed by Nonparametric Rate Smoothing
carnivora Carnivora body sizes and life history traits
nj Neighbor-Joining Tree Estimation
skyline Skyline Plot Estimate of Effective Population Size
vcv.phylo Phylogenetic Variance-covariance or Correlation Matrix
opsin Gene Tree of 32 opsin Sequences
corClasses Phylogenetic Correlation Structures
mantel.test Mantel Test for Similarity of Two Matrices
mcmc.popsize Reversible Jump MCMC to Infer Demographic History
dist.dna Pairwise Distances from DNA Sequences
which.edge Identifies Edges of a Tree
write.tree Write Tree File in Parenthetic Format
node.depth Depth of Nodes and Tips
xenarthra Molecular Phylogeny of Living Xenarthrans
multi2di Collapse and Resolve Multichotomies
pic Phylogenetically Independent Contrasts
dist.phylo Pairwise Distances from a Phylogenetic Tree
gammaStat Gamma-Statistic of Pybus and Harvey
theta.h Population Parameter THETA using Homozygosity
rotate Rotate an Internal Branch of a Tree
root Roots Phylogenetic Trees
plot.phylo Plot Phylogenies
woodmouse Cytochrome b Gene Sequences of Woodmice
read.nexus Read Tree File in Nexus Format
theta.k Population Parameter THETA using Expected Number of Alleles
nuc.div Nucleotide Diversity
plot.correlogramList Plot several Correlograms
hivtree Phylogenetic Tree of 193 HIV-1 Sequences
nodelabels Labelling the Nodes of a Tree
summary.phylo Print Summary of a Phylogeny
plot.correlogram Plot a Correlogram
write.nexus Write Tree File in Nexus Format
yule.cov Fits the Yule Model With Covariates
yule Fits Yule Model to a Phylogenetic Tree
No Results!

Last month downloads

Details

Date 2005-04-14
ZipData no
License GPL version 2 or newer
Packaged Fri Apr 15 20:45:11 2005; root

Include our badge in your README

[![Rdoc](http://www.rdocumentation.org/badges/version/ape)](http://www.rdocumentation.org/packages/ape)