ape v2.2-2
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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, 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 | |
| ace | Ancestral Character Estimation | |
| axisPhylo | Axis on Side of Phylogeny | |
| bd.ext | Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates | |
| NPRS.criterion | Objective Function Employed in Nonparametric Rate Smoothing | |
| Moran.I | Moran's I Autocorrelation Index | |
| add.scale.bar | Add a Scale Bar to a Phylogeny Plot | |
| compute.brlen | Branch Lengths Computation | |
| DNAbin | Manipulate DNA Sequences in Bit-Level Format | |
| carnivora | Carnivora body sizes and life history traits | |
| GC.content | Content in GC from DNA Sequences | |
| corBlomberg | Blomberg et al.'s Correlation Structure | |
| data.nex | NEXUS Data Example | |
| boot.phylo | Tree Bipartition and Bootstrapping Phylogenies | |
| evolve.phylo | Ancestral Character Simulation | |
| compar.lynch | Lynch's Comparative Method | |
| collapse.singles | Collapse Single Nodes | |
| hivtree | Phylogenetic Tree of 193 HIV-1 Sequences | |
| as.matching | Conversion Between Phylo and Matching Objects | |
| mlphylo | Estimating Phylogenies by Maximum Likelihood | |
| as.alignment | Conversion Among DNA Sequence Internal Formats | |
| klastorin | Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000) | |
| sh.test | Shimodaira-Hasegawa Test | |
| is.binary.tree | Test for Binary Tree | |
| compar.gee | Comparative Analysis with GEEs | |
| compar.cheverud | Cheverud's Comparative Method | |
| corMartins | Martins's (1997) Correlation Structure | |
| birthdeath | Estimation of Speciation and Extinction Rates With Birth-Death Models | |
| base.freq | Base frequencies from DNA Sequences | |
| mrca | Find Most Recent Common Ancestors Between Pairs | |
| vcv.phylo | Phylogenetic Variance-covariance or Correlation Matrix | |
| ape-internal | Internal Ape Functions | |
| dist.dna | Pairwise Distances from DNA Sequences | |
| node.depth | Depth of Nodes and Tips | |
| cophyloplot | Plots two phylogenetic trees face to face with links between the tips. | |
| dist.topo | Topological Distances Between Two Trees | |
| BIONJ | Tree Estimation Based on an Improved Version of the NJ Algorithm | |
| read.nexus | Read Tree File in Nexus Format | |
| ladderize | Ladderize a Tree | |
| FastME | Tree Estimation Based on the Minimum Evolution Algorithm | |
| howmanytrees | Calculate Numbers of Phylogenetic Trees | |
| nodelabels | Labelling the Nodes, Tips, and Edges of a Tree | |
| branching.times | Branching Times of a Phylogenetic Tree | |
| chiroptera | Bat Phylogeny | |
| corClasses | Phylogenetic Correlation Structures | |
| as.phylo | Conversion Among Tree Objects | |
| dist.gene | Pairwise Distances from Genetic Data | |
| Initialize.corPhyl | Initialize a 'corPhyl' Structure Object | |
| plot.phylo | Plot Phylogenies | |
| identify.phylo | Graphical Identification of Nodes and Tips | |
| DNAmodel | Defines Models of DNA Evolution | |
| heterozygosity | Heterozygosity at a Locus Using Gene Frequencies | |
| diversi.gof | Tests of Constant Diversification Rates | |
| print.phylo | Compact Display of a Phylogeny | |
| rtree | Generates Random Trees | |
| xenarthra | Molecular Phylogeny of Living Xenarthrans | |
| subtrees | All subtrees of a Phylogenetic Tree | |
| landplants | Gene Tree of 36 Landplant rbcL Sequences | |
| compar.ou | Ornstein--Uhlenbeck Model for Continuous Characters | |
| del.gaps | Delete Alignment Gaps in DNA Sequences | |
| plot.correlogram | Plot a Correlogram | |
| which.edge | Identifies Edges of a Tree | |
| mst | Minimum Spanning Tree | |
| corGrafen | Grafen's (1989) Correlation Structure | |
| bird.orders | Phylogeny of the Orders of Birds From Sibley and Ahlquist | |
| weight.taxo | Define Similarity Matrix | |
| corPagel | Pagel's ``lambda'' Correlation Structure | |
| matexpo | Matrix Exponential | |
| gammaStat | Gamma-Statistic of Pybus and Harvey | |
| consensus | Concensus Trees | |
| pic | Phylogenetically Independent Contrasts | |
| mcmc.popsize | Reversible Jump MCMC to Infer Demographic History | |
| drop.tip | Remove Tips in a Phylogenetic Tree | |
| chronoMPL | Molecular Dating With Mean Path Lengths | |
| ratogram | Ratogram Computed by Nonparametric Rate Smoothing | |
| is.ultrametric | Test if a Tree is Ultrametric | |
| plot.varcomp | Plot Variance Components | |
| woodmouse | Cytochrome b Gene Sequences of Woodmice | |
| read.nexus.data | Read Character Data In NEXUS Format | |
| read.dna | Read DNA Sequences in a File | |
| write.tree | Write Tree File in Parenthetic Format | |
| theta.s | Population Parameter THETA using Segregating Sites in DNA Sequences | |
| yule.cov | Fits the Yule Model With Covariates | |
| rotate | Swopping sister clades | |
| read.GenBank | Read DNA Sequences from GenBank via Internet | |
| theta.h | Population Parameter THETA using Homozygosity | |
| reorder.phylo | Internal Reordering of Trees | |
| ltt.plot | Lineages Through Time Plot | |
| bird.families | Phylogeny of the Families of Birds From Sibley and Ahlquist | |
| summary.phylo | Print Summary of a Phylogeny | |
| yule | Fits Yule Model to a Phylogenetic Tree | |
| coalescent.intervals | Coalescent Intervals | |
| read.caic | Read Tree File in CAIC Format | |
| nuc.div | Nucleotide Diversity | |
| write.nexus | Write Tree File in Nexus Format | |
| theta.k | Population Parameter THETA using Expected Number of Alleles | |
| read.tree | Read Tree File in Parenthetic Format | |
| skyline | Skyline Plot Estimate of Effective Population Size | |
| write.dna | Write DNA Sequences in a File | |
| as.phylo.formula | Conversion from Taxonomy Variables to Phylogenetic Trees | |
| chronopl | Molecular Dating With Penalized Likelihood | |
| correlogram.formula | Phylogenetic Correlogram | |
| multi2di | Collapse and Resolve Multichotomies | |
| phymltest | Fits a Bunch of Models with PhyML | |
| plot.ancestral | Plot Ancestral Character Values on a Tree | |
| corBrownian | Brownian Correlation Structure | |
| diversi.time | Analysis of Diversification with Survival Models | |
| balance | Balance of a Dichotomous Phylogenetic Tree | |
| subtreeplot | Zoom on a Portion of a Phylogeny by Successive Clicks | |
| bind.tree | Binds Trees | |
| varcomp | Compute Variance Component Estimates | |
| chronogram | Chronogram Computed by Nonparametric Rate Smoothing | |
| collapsed.intervals | Collapsed Coalescent Intervals | |
| mantel.test | Mantel Test for Similarity of Two Matrices | |
| seg.sites | Find Segregating Sites in DNA Sequences | |
| all.equal.phylo | Global Comparison of two Phylogenies | |
| nj | Neighbor-Joining Tree Estimation | |
| unique.multiPhylo | Revomes Duplicate Trees | |
| makeLabel | Label Management | |
| skylineplot | Drawing Skyline Plot Graphs | |
| zoom | Zoom on a Portion of a Phylogeny | |
| write.nexus.data | Write Character Data In NEXUS Format | |
| cherry | Number of Cherries and Null Models of Trees | |
| opsin | Gene Tree of 32 opsin Sequences | |
| root | Roots Phylogenetic Trees | |
| cophenetic.phylo | Pairwise Distances from a Phylogenetic Tree | |
| No Results! | ||
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Details
| Date | 2008-10-08 |
| ZipData | no |
| License | GPL (>= 2) |
| URL | http://ape.mpl.ird.fr/ |
| Packaged | Wed Oct 8 21:29:17 2008; paradis |
| depends | base (>= 2.6.0) , R (>= 2.6.0) |
| 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, Damien Vienne, Gangolf Jobb |
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