ape v1.0
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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, or the
population parameter theta based on various approaches.
Functions in ape
| Name | Description | |
| bird.orders | Phylogeny of the Orders of Birds From Sibley and Ahlquist | |
| compar.lynch | Lynch's Comparative Method | |
| branching.times | Branching Times of a Phylogenetic Tree | |
| pic | Phylogenetically Independent Contrasts | |
| theta.h | Population Parameter THETA using Homozygosity | |
| ape-internal | Internal Ape Functions | |
| dist.phylo | Pairwise Distances from a Phylogenetic Tree | |
| diversi.gof | Tests of Constant Diversification Rates | |
| ltt.plot | Lineages Through Time Plot | |
| base.freq | Base frequencies from DNA Sequences | |
| write.dna | Write DNA Sequences in a File | |
| mantel.test | Mantel Test for Similarity of Two Matrices | |
| read.nexus | Read Tree File in Nexus Format | |
| skylineplot | Drawing Skyline Plot Graphs | |
| compar.gee | Comparative Analysis with GEEs | |
| gamma.stat | Gamma-Statistic of Pybus and Harvey | |
| add.scale.bar | Add a Scale Bar to a Phylogeny Plot | |
| dist.dna | Pairwise Distances from DNA Sequences | |
| read.tree | Read Tree File in Parenthetic Format | |
| theta.k | Population Parameter THETA using Expected Number of Alleles | |
| bird.families | Phylogeny of the Families of Birds From Sibley and Ahlquist | |
| mst | Minimum Spanning Tree | |
| balance | Balance of a Dichotomous Phylogenetic Tree | |
| is.binary.tree | Test for Binary Tree | |
| dist.gene | Pairwise Distances from Genetic Data | |
| GC.content | Content in GC from DNA Sequences | |
| heterozygosity | Heterozygosity at a Locus Using Gene Frequencies | |
| write.tree | Write Tree File in Parenthetic Format | |
| is.ultrametric | Test if a Tree is Ultrametric | |
| read.dna | Read DNA Sequences in a File | |
| drop.tip | Remove Tips in a Phylogenetic Tree | |
| write.nexus | Write Tree File in Nexus Format | |
| skyline | Skyline Plot Estimate of Effective Population Size | |
| diversi.time | Analysis of Diversification with Survival Models | |
| cherry | Number of Cherries and Null Models of Trees | |
| hivtree | Phylogenetic Tree of 193 HIV-1 Sequences | |
| read.GenBank | Read DNA Sequences from GenBank via Internet | |
| collapsed.intervals | Collapsed Coalescent Intervals | |
| coalescent.intervals | Coalescent Intervals | |
| birthdeath | Estimation of Speciation and Extinction Rates With Birth-Death Models | |
| bind.tree | Binds Trees | |
| vcv.phylo | Phylogenetic Variance-covariance or Correlation Matrix | |
| plot.phylo | Plot Phylogenies | |
| theta.s | Population Parameter THETA using Segregating Sites in DNA Sequences | |
| all.equal.phylo | Global Comparison of two Phylogenies | |
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Details
| Date | 2003-2-23 |
| License | GPL version 2 or newer |
| depends | gee |
| Contributors | Emmanuel Paradis |
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