https://github.com/cran/ape
Tip revision: 2055920f8fef4d50e3aca374d5ee499aa93f3f1c authored by Emmanuel Paradis on 17 December 2003, 00:00:00 UTC
version 1.2
version 1.2
Tip revision: 2055920
INDEX
add.scale.bar Add a Scale Bar to a Phylogeny Plot
all.equal.phylo Global Comparison of two Phylogenies
as.phylo Conversion between "phylo" and "hclust" trees
balance Balance of a Dichotomous Phylogenetic Tree
base.freq Base frequencies from DNA Sequences
bind.tree Binds Trees
bird.families Phylogeny of the Families of Birds From Sibley
and Ahlquist
bird.orders Phylogeny of the Orders of Birds From Sibley
and Ahlquist
birthdeath Estimation of Speciation and Extinction Rates
With Birth-Death Models
branching.times Branching Times of a Phylogenetic Tree
cherry Number of Cherries and Null Models of Trees
chiroptera Bat Phylogeny
chronogram Chronogram Computed by Nonparametric Rate
Smoothing
coalescent.intervals Coalescent Intervals
collapsed.intervals Collapsed Coalescent Intervals
compar.gee Comparative Analysis with GEEs
compar.lynch Lynch's Comparative Method
dist.dna Pairwise Distances from DNA Sequences
dist.gene Pairwise Distances from Genetic Data
dist.phylo Pairwise Distances from a Phylogenetic Tree
diversi.gof Tests of Constant Diversification Rates
diversi.time Analysis of Diversification with Survival
Models
drop.tip Remove Tips in a Phylogenetic Tree
gammaStat Gamma-Statistic of Pybus and Harvey
GC.content Content in GC from DNA Sequences
heterozygosity Heterozygosity at a Locus Using Gene
Frequencies
hivtree Phylogenetic Tree of 193 HIV-1 Sequences
is.binary.tree Test for Binary Tree
is.ultrametric Test if a Tree is Ultrametric
klastorin Klastorin's (1982) method for classifying
genes as suggested by Misawa and Tajima (2000)
landplants Gene Tree of 36 Landplant rbcL Sequences
ltt.plot Lineages Through Time Plot
mantel.test Mantel Test for Similarity of Two Matrices
mst Minimum Spanning Tree
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
opsin Gene Tree of 32 opsin Sequences
pic Phylogenetically Independent Contrasts
plot.phylo Plot Phylogenies
ratogram Ratogram Computed by Nonparametric Rate
Smoothing
read.dna Read DNA Sequences in a File
read.GenBank Read DNA Sequences from GenBank via Internet
read.nexus Read Tree File in Nexus Format
read.tree Read Tree File in Parenthetic Format
skyline Skyline Plot Estimate of Effective Population
Size
skylineplot Drawing Skyline Plot Graphs
summary.phylo Print Summary of a Phylogeny
theta.h Population Parameter THETA using Homozygosity
theta.k Population Parameter THETA using Expected
Number of Alleles
theta.s Population Parameter THETA using Segregating
Sites in DNA Sequences
vcv.phylo Phylogenetic Variance-covariance or
Correlation Matrix
woodmouse Cytochrome b Sequences of Woodmice
write.dna Write DNA Sequences in a File
write.nexus Write Tree File in Nexus Format
write.tree Write Tree File in Parenthetic Format
xenarthra Molecular Phylogeny of Living Xenarthrans
yule Fits Yule Model to a Phylogenetic Tree
zoom Zoom on a Portion of a Phylogeny