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

Date 2004-03-19
License GPL version 2 or newer
depends gee
Contributors Emmanuel Paradis

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