ape v2.1-1
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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, nucleotide diversity,
generalized skyline plots, estimation of absolute evolutionary rates
and clock-like trees using mean path lengths, non-parametric rate
smoothing and penalized likelihood, classifying genes in trees using
the Klastorin-Misawa-Tajima approach. Phylogeny estimation can be done
with the NJ, BIONJ, ME, and ML methods.
Functions in ape
| Name | Description | |
| birthdeath | Estimation of Speciation and Extinction Rates With Birth-Death Models | |
| axisPhylo | Axis on Side of Phylogeny | |
| bird.families | Phylogeny of the Families of Birds From Sibley and Ahlquist | |
| bind.tree | Binds Trees | |
| is.ultrametric | Test if a Tree is Ultrametric | |
| drop.tip | Remove Tips in a Phylogenetic Tree | |
| bd.ext | Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates | |
| collapse.singles | Collapse Single Nodes | |
| BIONJ | Tree Estimation Based on an Improved Version of the NJ Algorithm | |
| chronopl | Molecular Dating With Penalized Likelihood | |
| read.GenBank | Read DNA Sequences from GenBank via Internet | |
| ape-internal | Internal Ape Functions | |
| consensus | Concensus Trees | |
| carnivora | Carnivora body sizes and life history traits | |
| base.freq | Base frequencies from DNA Sequences | |
| compar.cheverud | Cheverud's Comparative Method | |
| cherry | Number of Cherries and Null Models of Trees | |
| read.nexus.data | Read Character Data In NEXUS Format | |
| compute.brlen | Branch Lengths Computation | |
| is.binary.tree | Test for Binary Tree | |
| chronogram | Chronogram Computed by Nonparametric Rate Smoothing | |
| DNAbin | Manipulate DNA Sequences in Bit-Level Format | |
| DNAmodel | Defines Models of DNA Evolution | |
| NPRS.criterion | Objective Function Employed in Nonparametric Rate Smoothing | |
| collapsed.intervals | Collapsed Coalescent Intervals | |
| opsin | Gene Tree of 32 opsin Sequences | |
| ltt.plot | Lineages Through Time Plot | |
| bird.orders | Phylogeny of the Orders of Birds From Sibley and Ahlquist | |
| boot.phylo | Tree Bipartition and Bootstrapping Phylogenies | |
| summary.phylo | Print Summary of a Phylogeny | |
| Initialize.corPhyl | Initialize a 'corPhyl' Structure Object | |
| compar.ou | Ornstein--Uhlenbeck Model for Continuous Characters | |
| mrca | Find Most Recent Common Ancestors Between Pairs | |
| root | Roots Phylogenetic Trees | |
| gammaStat | Gamma-Statistic of Pybus and Harvey | |
| yule.cov | Fits the Yule Model With Covariates | |
| hivtree | Phylogenetic Tree of 193 HIV-1 Sequences | |
| unique.multiPhylo | Revomes Duplicate Trees | |
| coalescent.intervals | Coalescent Intervals | |
| Moran.I | Moran's I Autocorrelation Index | |
| ace | Ancestral Character Estimation | |
| evolve.phylo | Ancestral Character Simulation | |
| all.equal.phylo | Global Comparison of two Phylogenies | |
| mcmc.popsize | Reversible Jump MCMC to Infer Demographic History | |
| multi2di | Collapse and Resolve Multichotomies | |
| mantel.test | Mantel Test for Similarity of Two Matrices | |
| klastorin | Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000) | |
| compar.lynch | Lynch's Comparative Method | |
| howmanytrees | Calculate Numbers of Phylogenetic Trees | |
| compar.gee | Comparative Analysis with GEEs | |
| yule | Fits Yule Model to a Phylogenetic Tree | |
| matexpo | Matrix Exponential | |
| write.dna | Write DNA Sequences in a File | |
| corBrownian | Brownian Correlation Structure | |
| corGrafen | Grafen's (1989) Correlation Structure | |
| plot.phylo | Plot Phylogenies | |
| GC.content | Content in GC from DNA Sequences | |
| as.phylo | Conversion Among Tree Objects | |
| nodelabels | Labelling the Nodes, Tips, and Edges of a Tree | |
| corClasses | Phylogenetic Correlation Structures | |
| write.tree | Write Tree File in Parenthetic Format | |
| rtree | Generates Random Trees | |
| plot.varcomp | Plot Variance Components | |
| mst | Minimum Spanning Tree | |
| print.phylo | Compact Display of a Phylogeny | |
| dist.topo | Topological Distances Between Two Trees | |
| diversi.gof | Tests of Constant Diversification Rates | |
| read.nexus | Read Tree File in Nexus Format | |
| read.tree | Read Tree File in Parenthetic Format | |
| zoom | Zoom on a Portion of a Phylogeny | |
| corMartins | Martins's (1997) Correlation Structure | |
| dist.gene | Pairwise Distances from Genetic Data | |
| ladderize | Ladderize a Tree | |
| as.phylo.formula | Conversion from Taxonomy Variables to Phylogenetic Trees | |
| heterozygosity | Heterozygosity at a Locus Using Gene Frequencies | |
| cophenetic.phylo | Pairwise Distances from a Phylogenetic Tree | |
| plot.correlogram | Plot a Correlogram | |
| skylineplot | Drawing Skyline Plot Graphs | |
| xenarthra | Molecular Phylogeny of Living Xenarthrans | |
| skyline | Skyline Plot Estimate of Effective Population Size | |
| woodmouse | Cytochrome b Gene Sequences of Woodmice | |
| read.dna | Read DNA Sequences in a File | |
| pic | Phylogenetically Independent Contrasts | |
| vcv.phylo | Phylogenetic Variance-covariance or Correlation Matrix | |
| nuc.div | Nucleotide Diversity | |
| read.caic | Read Tree File in CAIC Format | |
| seg.sites | Find Segregating Sites in DNA Sequences | |
| identify.phylo | Graphical Identification of Nodes and Tips | |
| sh.test | Shimodaira-Hasegawa Test | |
| theta.k | Population Parameter THETA using Expected Number of Alleles | |
| nj | Neighbor-Joining Tree Estimation | |
| FastME | Tree Estimation Based on the Minimum Evolution Algorithm | |
| reorder.phylo | Internal Reordering of Trees | |
| phymltest | Fits a Bunch of Models with PHYML | |
| plot.ancestral | Plot Ancestral Character Values on a Tree | |
| chiroptera | Bat Phylogeny | |
| rotate | Swopping sister clades | |
| ratogram | Ratogram Computed by Nonparametric Rate Smoothing | |
| mlphylo | Estimating Phylogenies by Maximum Likelihood | |
| theta.h | Population Parameter THETA using Homozygosity | |
| node.depth | Depth of Nodes and Tips | |
| chronoMPL | Molecular Dating With Mean Path Lengths | |
| as.alignment | Conversion Among DNA Sequence Internal Formats | |
| diversi.time | Analysis of Diversification with Survival Models | |
| add.scale.bar | Add a Scale Bar to a Phylogeny Plot | |
| balance | Balance of a Dichotomous Phylogenetic Tree | |
| correlogram.formula | Phylogenetic Correlogram | |
| dist.dna | Pairwise Distances from DNA Sequences | |
| theta.s | Population Parameter THETA using Segregating Sites in DNA Sequences | |
| write.nexus.data | Write Character Data In NEXUS Format | |
| weight.taxo | Define Similarity Matrix | |
| as.matching | Conversion Between Phylo and Matching Objects | |
| branching.times | Branching Times of a Phylogenetic Tree | |
| data.nex | NEXUS Data Example | |
| which.edge | Identifies Edges of a Tree | |
| varcomp | Compute Variance Component Estimates | |
| write.nexus | Write Tree File in Nexus Format | |
| landplants | Gene Tree of 36 Landplant rbcL Sequences | |
| No Results! | ||
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Details
| Date | 2008-02-01 |
| ZipData | no |
| License | GPL (>= 2) |
| URL | http://pbil.univ-lyon1.fr/R/ape/ |
| Packaged | Fri Feb 1 14:17:29 2008; paradis |
| depends | base (>= 2.0.0) , R (>= 2.0.0) |
| suggests | gee , lattice , nlme |
| Contributors | Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Cuong, Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel, Christoph Heibl, Vincent Lefort, Jim Lemon, Yvonnick Noel, Johan Nylander, Rainer Opgen-Rhein, Korbinian Strimmer, Gangolf Jobb |
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