ape v0.2-1
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Analyses of Phylogenetics and Evolution
Ape provides functions for reading, writing, and plotting
phylogenetic trees in parenthetic format (standard Newick format),
analyses of comparative data in a phylogenetic framework, analyses of
diversification and macroevolution, computing distances from allelic
and nucleotide data, reading nucleotide sequences from GenBank via
internet, 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 | |
| balance | Balance of a Dichotomous Phylogenetic Tree | |
| base.freq | Base frequencies from DNA Sequences | |
| compar.lynch | Lynch's Comparative Method | |
| branching.times | Branching Times of a Phylogenetic Tree | |
| ltt.plot | Lineages Through Time Plot | |
| read.GenBank | Read DNA Sequences from GenBank via Internet | |
| theta.s | Population Parameter THETA using Segregating Sites in DNA Sequences | |
| pic | Phylogenetically Independent Contrasts | |
| cherry | Number of Cherries and Null Models of Trees | |
| read.tree | Read Tree File in Parenthetic Format | |
| heterozygosity | Heterozygosity at a Locus Using Gene Frequencies | |
| dist.phylo | Pairwise Distances from a Phylogenetic Tree | |
| birthdeath | Estimation of Speciation and Extinction Rates With Birth-Death Models | |
| theta.h | Population Parameter THETA using Homozygosity | |
| vcv.phylo | Phylogenetic Variance-covariance or Correlation Matrix | |
| plot.phylo | Plot Phylogenies | |
| bird.families | Phylogeny of the Families of Birds From Sibley and Ahlquist | |
| GC.content | Content in GC from DNA Sequences | |
| ape-internal | Internal Ape Functions | |
| is.binary.tree | Test for Binary Tree | |
| coalescent.intervals | Coalescent Intervals | |
| mst | Minimum Spanning Tree | |
| theta.k | Population Parameter THETA using Expected Number of Alleles | |
| hivtree | Phylogenetic Tree of 193 HIV-1 Sequences | |
| collapsed.intervals | Collapsed Coalescent Intervals | |
| mantel.test | Mantel Test for Similarity of Two Matrices | |
| dist.gene | Pairwise Distances from Genetic Data | |
| write.tree | Write Tree File in Parenthetic Format | |
| diversi.gof | Tests of Constant Diversification Rates | |
| dist.dna | Pairwise Distances from DNA Sequences | |
| diversi.time | Analysis of Diversification with Survival Models | |
| add.scale.bar | Add a Scale Bar to a Phylogeny Plot | |
| gamma.stat | Gamma-Statistic of Pybus and Harvey | |
| skylineplot | Drawing Skyline Plot Graphs | |
| compar.gee | Comparative Analysis with GEEs | |
| all.equal.phylo | Global Comparison of two Phylogenies | |
| skyline | Skyline Plot Estimate of Effective Population Size | |
| No Results! | ||
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Details
| Date | 2002-10-28 |
| License | GPL version 2 or newer |
| depends | base (>= 1.4.1) , gee , R (>= 1.4.1) |
| Contributors | Emmanuel Paradis |
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