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Analyses of Phylogenetics and Evolution
Ape provides functions for reading, 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 | |
| diversi.time | Analysis of Diversification with Survival Models | |
| vcv.phylo | Phylogenetic Variance-covariance or Correlation Matrix | |
| GC.content | Content in GC from DNA Sequences | |
| compar.lynch | Lynch's Comparative Method | |
| dist.gene | Pairwise Distances from Genetic Data | |
| dist.dna | Pairwise Distances from DNA Sequences | |
| ape-internal | Internal Ape Functions | |
| all.equal.phylo | Global Comparison of two Phylogenies | |
| compar.gee | Comparative Analysis with GEEs | |
| mantel.test | Mantel Test for Similarity of Two Matrices | |
| theta.s | Population Parameter THETA using Segregating Sites in DNA Sequences | |
| balance | Balance of a Dichotomous Phylogenetic Tree | |
| theta.k | Population Parameter THETA using Expected Number of Alleles | |
| pic | Phylogenetically Independent Contrasts | |
| cherry | Number of Cherries and Null Models of Trees | |
| read.tree | Read Tree File in Parenthetic Format | |
| skyline.plot | Skyline Plot of Estimated Effective Population Size | |
| heterozygosity | Heterozygosity at a Locus Using Gene Frequencies | |
| diversi.gof | Tests of Constant Diversification Rates | |
| gamma.stat | Gamma-Statistic of Pybus and Harvey | |
| branching.times | Branching Times of a Phylogenetic Tree | |
| base.freq | Base frequencies from DNA Sequences | |
| theta.h | Population Parameter THETA using Homozigosity | |
| ltt.plot | Lineages Through Time Plot | |
| plot.phylo | Plot Phylogenies | |
| read.GenBank | Read DNA Sequences from GenBank via Internet | |
| dist.phylo | Pairwise Distances from a Phylogenetic Tree | |
| mst | Minimum Spanning Tree | |
| No Results! | ||
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Details
| Date | 2002-08-27 |
| License | GPL version 2 or newer |
| depends | base (>= 1.4.1) , gee , R (>= 1.4.1) |
| Contributors | Emmanuel Paradis |
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