https://github.com/cran/ape
Tip revision: 88b62374d892f92ecd45527da6fe3aefd5eb8f3e authored by Emmanuel Paradis on 20 September 2002, 00:00:00 UTC
version 0.2
version 0.2
Tip revision: 88b6237
INDEX
GC.content Content in GC from DNA Sequences
add.scale.bar Add a Scale Bar to a Phylogeny Plot
all.equal.phylo Global Comparison of two Phylogenies
ape-internal Internal Ape Functions
balance Balance of a Dichotomous Phylogenetic Tree
base.freq Base frequencies from DNA Sequences
bird.families Phylogeny of the Families 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
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
gamma.stat Gamma-Statistic of Pybus and Harvey
heterozygosity Heterozygosity at a Locus Using Gene
Frequencies
hivtree Phylogenetic Tree of 193 HIV-1 Sequences
is.binary.tree Test for Binary Tree
ltt.plot Lineages Through Time Plot
mantel.test Mantel Test for Similarity of Two Matrices
mst Minimum Spanning Tree
pic Phylogenetically Independent Contrasts
plot.phylo Plot Phylogenies
read.GenBank Read DNA Sequences from GenBank via Internet
read.tree Read Tree File in Parenthetic Format
skyline Skyline Plot Estimate of Effective Population
Size
skylineplot Drawing Skyline Plot Graphs
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
write.tree Write Tree File in Parenthetic Format