ape v2.0-1
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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 | |
| bd.ext | Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates | |
| multi2di | Collapse and Resolve Multichotomies | |
| plot.ancestral | Plot Ancestral Character Values on a Tree | |
| pic | Phylogenetically Independent Contrasts | |
| Moran.I | Moran's I Autocorrelation Index | |
| rtree | Generates Random Trees | |
| branching.times | Branching Times of a Phylogenetic Tree | |
| compar.cheverud | Cheverud's Comparative Method | |
| base.freq | Base frequencies from DNA Sequences | |
| plot.correlogram | Plot a Correlogram | |
| node.depth | Depth of Nodes and Tips | |
| write.tree | Write Tree File in Parenthetic Format | |
| skylineplot | Drawing Skyline Plot Graphs | |
| compute.brlen | Branch Lengths Computation | |
| nodelabels | Labelling the Nodes, Tips, and Edges of a Tree | |
| skyline | Skyline Plot Estimate of Effective Population Size | |
| chiroptera | Bat Phylogeny | |
| data.nex | NEXUS Data Example | |
| ratogram | Ratogram Computed by Nonparametric Rate Smoothing | |
| plot.varcomp | Plot Variance Components | |
| woodmouse | Cytochrome b Gene Sequences of Woodmice | |
| xenarthra | Molecular Phylogeny of Living Xenarthrans | |
| as.phylo | Conversion Among Tree Objects | |
| diversi.gof | Tests of Constant Diversification Rates | |
| theta.s | Population Parameter THETA using Segregating Sites in DNA Sequences | |
| evolve.phylo | Ancestral Character Simulation | |
| consensus | Concensus Trees | |
| corClasses | Phylogenetic Correlation Structures | |
| NPRS.criterion | Objective Function Employed in Nonparametric Rate Smoothing | |
| is.binary.tree | Test for Binary Tree | |
| klastorin | Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000) | |
| mrca | Find Most Recent Common Ancestors Between Pairs | |
| seg.sites | Find Segregating Sites in DNA Sequences | |
| yule.cov | Fits the Yule Model With Covariates | |
| write.nexus.data | Write Character Data In NEXUS Format | |
| mantel.test | Mantel Test for Similarity of Two Matrices | |
| ace | Ancestral Character Estimation | |
| ape-internal | Internal Ape Functions | |
| collapse.singles | Collapse Single Nodes | |
| cherry | Number of Cherries and Null Models of Trees | |
| discrete.dist | Taxonomic Level from a Pairwise Distances Matrix | |
| chronoMPL | Molecular Dating With Mean Path Lengths | |
| nj | Neighbor-Joining Tree Estimation | |
| ltt.plot | Lineages Through Time Plot | |
| as.phylo.formula | Conversion from Taxonomy Variables to Phylogenetic Trees | |
| bird.orders | Phylogeny of the Orders of Birds From Sibley and Ahlquist | |
| bird.families | Phylogeny of the Families of Birds From Sibley and Ahlquist | |
| BIONJ | Tree Estimation Based on an Improved Version of the NJ Algorithm | |
| coalescent.intervals | Coalescent Intervals | |
| corBrownian | Brownian Correlation Structure | |
| chronopl | Molecular Dating With Penalized Likelihood | |
| diversi.time | Analysis of Diversification with Survival Models | |
| DNAbin | Manipulate DNA Sequences in Bit-Level Format | |
| phymltest | Fits a Bunch of Models with PHYML | |
| hivtree | Phylogenetic Tree of 193 HIV-1 Sequences | |
| varcomp | Compute Variance Component Estimates | |
| root | Roots Phylogenetic Trees | |
| which.edge | Identifies Edges of a Tree | |
| dist.dna | Pairwise Distances from DNA Sequences | |
| write.nexus | Write Tree File in Nexus Format | |
| drop.tip | Remove Tips in a Phylogenetic Tree | |
| mlphylo | Estimating Phylogenies by Maximum Likelihood | |
| nuc.div | Nucleotide Diversity | |
| read.nexus.data | Read Character Data In NEXUS Format | |
| gammaStat | Gamma-Statistic of Pybus and Harvey | |
| vcv.phylo | Phylogenetic Variance-covariance or Correlation Matrix | |
| read.GenBank | Read DNA Sequences from GenBank via Internet | |
| FastME | Tree Estimation Based on the Minimum Evolution Algorithm | |
| Initialize.corPhyl | Initialize a 'corPhyl' Structure Object | |
| heterozygosity | Heterozygosity at a Locus Using Gene Frequencies | |
| mcmc.popsize | Reversible Jump MCMC to Infer Demographic History | |
| panel.superpose.correlogram | Lattice panel used in 'plot.correlogramList'. | |
| print.phylo | Compact Display of a Phylogeny | |
| read.tree | Read Tree File in Parenthetic Format | |
| GC.content | Content in GC from DNA Sequences | |
| ladderize | Ladderize a Tree | |
| yule | Fits Yule Model to a Phylogenetic Tree | |
| balance | Balance of a Dichotomous Phylogenetic Tree | |
| birthdeath | Estimation of Speciation and Extinction Rates With Birth-Death Models | |
| chronogram | Chronogram Computed by Nonparametric Rate Smoothing | |
| howmanytrees | Calculate Numbers of Phylogenetic Trees | |
| compar.gee | Comparative Analysis with GEEs | |
| opsin | Gene Tree of 32 opsin Sequences | |
| DNAmodel | Defines Models of DNA Evolution | |
| dist.gene | Pairwise Distances from Genetic Data | |
| as.matching | Conversion Between Phylo and Matching Objects | |
| dist.topo | Topological Distances Between Two Trees | |
| landplants | Gene Tree of 36 Landplant rbcL Sequences | |
| all.equal.phylo | Global Comparison of two Phylogenies | |
| rotate | Swopping sister clades | |
| carnivora | Carnivora body sizes and life history traits | |
| boot.phylo | Tree Bipartition and Bootstrapping Phylogenies | |
| plot.phylo | Plot Phylogenies | |
| plot.correlogramList | Plot several Correlograms | |
| sh.test | Shimodaira-Hasegawa Test | |
| read.dna | Read DNA Sequences in a File | |
| theta.h | Population Parameter THETA using Homozygosity | |
| write.dna | Write DNA Sequences in a File | |
| Correlogram | Compute a correlogram | |
| reorder.phylo | Internal Reordering of Trees | |
| summary.phylo | Print Summary of a Phylogeny | |
| add.scale.bar | Add a Scale Bar to a Phylogeny Plot | |
| as.alignment | Conversion Among DNA Sequence Internal Formats | |
| axisPhylo | Axis on Side of Phylogeny | |
| bind.tree | Binds Trees | |
| compar.ou | Ornstein--Uhlenbeck Model for Continuous Characters | |
| compar.lynch | Lynch's Comparative Method | |
| cophenetic.phylo | Pairwise Distances from a Phylogenetic Tree | |
| collapsed.intervals | Collapsed Coalescent Intervals | |
| corGrafen | Grafen's (1989) Correlation Structure | |
| is.ultrametric | Test if a Tree is Ultrametric | |
| read.caic | Read Tree File in CAIC Format | |
| corMartins | Martins's (1997) Correlation Structure | |
| mst | Minimum Spanning Tree | |
| read.nexus | Read Tree File in Nexus Format | |
| theta.k | Population Parameter THETA using Expected Number of Alleles | |
| weight.taxo | Pairwise Distances from a Taxonomic Level | |
| zoom | Zoom on a Portion of a Phylogeny | |
| matexpo | Matrix Exponential | |
| unique.multi.tree | Revomes Duplicate Trees | |
| No Results! | ||
Last month downloads
Details
| Date | 2007-09-05 |
| ZipData | no |
| License | GPL version 2 or newer |
| URL | http://pbil.univ-lyon1.fr/R/ape/ |
| Packaged | Fri Sep 7 15:16:46 2007; 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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