ape v1.2-3
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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 | |
| GC.content | Content in GC from DNA Sequences | |
| balance | Balance of a Dichotomous Phylogenetic Tree | |
| NPRS.criterion | Objective Function Employed in Nonparametric Rate Smoothing | |
| cherry | Number of Cherries and Null Models of Trees | |
| bind.tree | Binds Trees | |
| dist.phylo | Pairwise Distances from a Phylogenetic Tree | |
| bird.orders | Phylogeny of the Orders of Birds From Sibley and Ahlquist | |
| plot.phylo | Plot Phylogenies | |
| heterozygosity | Heterozygosity at a Locus Using Gene Frequencies | |
| compar.lynch | Lynch's Comparative Method | |
| mst | Minimum Spanning Tree | |
| opsin | Gene Tree of 32 opsin Sequences | |
| ape-internal | Internal Ape Functions | |
| mantel.test | Mantel Test for Similarity of Two Matrices | |
| node.depth.edgelength | Distance from Root to Nodes and Tips | |
| hivtree | Phylogenetic Tree of 193 HIV-1 Sequences | |
| drop.tip | Remove Tips in a Phylogenetic Tree | |
| coalescent.intervals | Coalescent Intervals | |
| diversi.gof | Tests of Constant Diversification Rates | |
| is.binary.tree | Test for Binary Tree | |
| gammaStat | Gamma-Statistic of Pybus and Harvey | |
| klastorin | Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000) | |
| all.equal.phylo | Global Comparison of two Phylogenies | |
| dist.dna | Pairwise Distances from DNA Sequences | |
| node.depth | Depth of Nodes and Tips | |
| chiroptera | Bat Phylogeny | |
| as.phylo | Conversion between "phylo" and "hclust" trees | |
| skyline | Skyline Plot Estimate of Effective Population Size | |
| chronogram | Chronogram Computed by Nonparametric Rate Smoothing | |
| read.dna | Read DNA Sequences in a File | |
| dist.gene | Pairwise Distances from Genetic Data | |
| branching.times | Branching Times of a Phylogenetic Tree | |
| base.freq | Base frequencies from DNA Sequences | |
| xenarthra | Molecular Phylogeny of Living Xenarthrans | |
| summary.phylo | Print Summary of a Phylogeny | |
| zoom | Zoom on a Portion of a Phylogeny | |
| theta.s | Population Parameter THETA using Segregating Sites in DNA Sequences | |
| read.nexus | Read Tree File in Nexus Format | |
| theta.h | Population Parameter THETA using Homozygosity | |
| write.tree | Write Tree File in Parenthetic Format | |
| add.scale.bar | Add a Scale Bar to a Phylogeny Plot | |
| seg.sites | Find Segregating Sites in DNA Sequences | |
| birthdeath | Estimation of Speciation and Extinction Rates With Birth-Death Models | |
| ltt.plot | Lineages Through Time Plot | |
| is.ultrametric | Test if a Tree is Ultrametric | |
| pic | Phylogenetically Independent Contrasts | |
| compar.gee | Comparative Analysis with GEEs | |
| bird.families | Phylogeny of the Families of Birds From Sibley and Ahlquist | |
| write.dna | Write DNA Sequences in a File | |
| skylineplot | Drawing Skyline Plot Graphs | |
| read.GenBank | Read DNA Sequences from GenBank via Internet | |
| vcv.phylo | Phylogenetic Variance-covariance or Correlation Matrix | |
| yule | Fits Yule Model to a Phylogenetic Tree | |
| landplants | Gene Tree of 36 Landplant rbcL Sequences | |
| read.tree | Read Tree File in Parenthetic Format | |
| theta.k | Population Parameter THETA using Expected Number of Alleles | |
| ratogram | Ratogram Computed by Nonparametric Rate Smoothing | |
| collapsed.intervals | Collapsed Coalescent Intervals | |
| woodmouse | Cytochrome b Sequences of Woodmice | |
| write.nexus | Write Tree File in Nexus Format | |
| diversi.time | Analysis of Diversification with Survival Models | |
| rtree | Generates Random Trees | |
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Details
| Date | 2004-05-24 |
| License | GPL version 2 or newer |
| Packaged | Mon May 24 00:31:49 2004; PARADYS |
| depends | gee |
| Contributors | Emmanuel Paradis |
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