ape v1.1-2
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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 | |
| add.scale.bar | Add a Scale Bar to a Phylogeny Plot | |
| coalescent.intervals | Coalescent Intervals | |
| all.equal.phylo | Global Comparison of two Phylogenies | |
| heterozygosity | Heterozygosity at a Locus Using Gene Frequencies | |
| theta.s | Population Parameter THETA using Segregating Sites in DNA Sequences | |
| compar.gee | Comparative Analysis with GEEs | |
| hivtree | Phylogenetic Tree of 193 HIV-1 Sequences | |
| compar.lynch | Lynch's Comparative Method | |
| ltt.plot | Lineages Through Time Plot | |
| plot.phylo | Plot Phylogenies | |
| summary.phylo | Print Summary of a Phylogeny | |
| klastorin | Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000) | |
| NPRS.criterion | Objective Function Employed in Nonparametric Rate Smoothing | |
| diversi.time | Analysis of Diversification with Survival Models | |
| read.dna | Read DNA Sequences in a File | |
| cherry | Number of Cherries and Null Models of Trees | |
| read.tree | Read Tree File in Parenthetic Format | |
| vcv.phylo | Phylogenetic Variance-covariance or Correlation Matrix | |
| chronogram | Chronogram Computed by Nonparametric Rate Smoothing | |
| bind.tree | Binds Trees | |
| ape-internal | Internal Ape Functions | |
| opsin | Gene Tree of 32 opsin Sequences | |
| landplants | Gene Tree of 36 Landplant rbcL Sequences | |
| drop.tip | Remove Tips in a Phylogenetic Tree | |
| theta.k | Population Parameter THETA using Expected Number of Alleles | |
| write.dna | Write DNA Sequences in a File | |
| write.nexus | Write Tree File in Nexus Format | |
| woodmouse | Cytochrome b Sequences of Woodmice | |
| theta.h | Population Parameter THETA using Homozygosity | |
| is.ultrametric | Test if a Tree is Ultrametric | |
| bird.orders | Phylogeny of the Orders of Birds From Sibley and Ahlquist | |
| mantel.test | Mantel Test for Similarity of Two Matrices | |
| birthdeath | Estimation of Speciation and Extinction Rates With Birth-Death Models | |
| dist.gene | Pairwise Distances from Genetic Data | |
| gamma.stat | Gamma-Statistic of Pybus and Harvey | |
| diversi.gof | Tests of Constant Diversification Rates | |
| GC.content | Content in GC from DNA Sequences | |
| read.nexus | Read Tree File in Nexus Format | |
| skylineplot | Drawing Skyline Plot Graphs | |
| ratogram | Ratogram Computed by Nonparametric Rate Smoothing | |
| dist.dna | Pairwise Distances from DNA Sequences | |
| write.tree | Write Tree File in Parenthetic Format | |
| base.freq | Base frequencies from DNA Sequences | |
| balance | Balance of a Dichotomous Phylogenetic Tree | |
| as.phylo | Conversion between "phylo" and "hclust" trees | |
| collapsed.intervals | Collapsed Coalescent Intervals | |
| bird.families | Phylogeny of the Families of Birds From Sibley and Ahlquist | |
| skyline | Skyline Plot Estimate of Effective Population Size | |
| branching.times | Branching Times of a Phylogenetic Tree | |
| pic | Phylogenetically Independent Contrasts | |
| dist.phylo | Pairwise Distances from a Phylogenetic Tree | |
| mst | Minimum Spanning Tree | |
| xenarthra | Molecular Phylogeny of Living Xenarthrans | |
| read.GenBank | Read DNA Sequences from GenBank via Internet | |
| is.binary.tree | Test for Binary Tree | |
| No Results! | ||
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Details
| Date | 2003-07-11 |
| License | GPL version 2 or newer |
| depends | gee |
| Contributors | Emmanuel Paradis |
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