ape v2.3-3
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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,
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. Phylogeny estimation can be done with the NJ,
BIONJ, and ME methods.
Functions in ape
| Name | Description | |
| DNAbin | Manipulate DNA Sequences in Bit-Level Format | |
| compar.gee | Comparative Analysis with GEEs | |
| bird.orders | Phylogeny of the Orders of Birds From Sibley and Ahlquist | |
| heterozygosity | Heterozygosity at a Locus Using Gene Frequencies | |
| landplants | Gene Tree of 36 Landplant rbcL Sequences | |
| ltt.plot | Lineages Through Time Plot | |
| BIONJ | Tree Estimation Based on an Improved Version of the NJ Algorithm | |
| matexpo | Matrix Exponential | |
| plot.correlogram | Plot a Correlogram | |
| balance | Balance of a Dichotomous Phylogenetic Tree | |
| base.freq | Base frequencies from DNA Sequences | |
| read.GenBank | Read DNA Sequences from GenBank via Internet | |
| GC.content | Content in GC from DNA Sequences | |
| chronogram | Chronogram Computed by Nonparametric Rate Smoothing | |
| chronoMPL | Molecular Dating With Mean Path Lengths | |
| coalescent.intervals | Coalescent Intervals | |
| theta.h | Population Parameter THETA using Homozygosity | |
| add.scale.bar | Add a Scale Bar to a Phylogeny Plot | |
| all.equal.phylo | Global Comparison of two Phylogenies | |
| bind.tree | Binds Trees | |
| boot.phylo | Tree Bipartition and Bootstrapping Phylogenies | |
| data.nex | NEXUS Data Example | |
| Initialize.corPhyl | Initialize a `corPhyl' Structure Object | |
| is.ultrametric | Test if a Tree is Ultrametric | |
| Moran.I | Moran's I Autocorrelation Index | |
| ace | Ancestral Character Estimation | |
| makeLabel | Label Management | |
| compar.cheverud | Cheverud's Comparative Method | |
| NPRS.criterion | Objective Function Employed in Nonparametric Rate Smoothing | |
| collapse.singles | Collapse Single Nodes | |
| ladderize | Ladderize a Tree | |
| ape-package | Analyses of Phylogenetics and Evolution | |
| compar.ou | Ornstein--Uhlenbeck Model for Continuous Characters | |
| hivtree | Phylogenetic Tree of 193 HIV-1 Sequences | |
| cophyloplot | Plots two phylogenetic trees face to face with links between the tips. | |
| identify.phylo | Graphical Identification of Nodes and Tips | |
| FastME | Tree Estimation Based on the Minimum Evolution Algorithm | |
| corBrownian | Brownian Correlation Structure | |
| mst | Minimum Spanning Tree | |
| is.monophyletic | Is Group Monophyletic | |
| mrca | Find Most Recent Common Ancestors Between Pairs | |
| nodelabels | Labelling the Nodes, Tips, and Edges of a Tree | |
| consensus | Concensus Trees | |
| mat5M3ID | Five Trees | |
| read.caic | Read Tree File in CAIC Format | |
| read.nexus.data | Read Character Data In NEXUS Format | |
| node.depth | Depth of Nodes and Tips | |
| plot.ancestral | Plot Ancestral Character Values on a Tree | |
| as.phylo.formula | Conversion from Taxonomy Variables to Phylogenetic Trees | |
| dist.topo | Topological Distances Between Two Trees | |
| skylineplot | Drawing Skyline Plot Graphs | |
| axisPhylo | Axis on Side of Phylogeny | |
| unique.multiPhylo | Revomes Duplicate Trees | |
| chronopl | Molecular Dating With Penalized Likelihood | |
| nj | Neighbor-Joining Tree Estimation | |
| plot.varcomp | Plot Variance Components | |
| varcomp | Compute Variance Component Estimates | |
| ratogram | Ratogram Computed by Nonparametric Rate Smoothing | |
| which.edge | Identifies Edges of a Tree | |
| woodmouse | Cytochrome b Gene Sequences of Woodmice | |
| corPagel | Pagel's ``lambda'' Correlation Structure | |
| write.nexus.data | Write Character Data In NEXUS Format | |
| plot.phylo | Plot Phylogenies | |
| write.dna | Write DNA Sequences in a File | |
| zoom | Zoom on a Portion of a Phylogeny | |
| summary.phylo | Print Summary of a Phylogeny | |
| corClasses | Phylogenetic Correlation Structures | |
| theta.s | Population Parameter THETA using Segregating Sites in DNA Sequences | |
| subtreeplot | Zoom on a Portion of a Phylogeny by Successive Clicks | |
| del.gaps | Delete Alignment Gaps in DNA Sequences | |
| phymltest | Fits a Bunch of Models with PhyML | |
| multi2di | Collapse and Resolve Multichotomies | |
| root | Roots Phylogenetic Trees | |
| skyline | Skyline Plot Estimate of Effective Population Size | |
| mat5Mrand | Five Independent Trees | |
| rotate | Swapping sister clades | |
| theta.k | Population Parameter THETA using Expected Number of Alleles | |
| write.nexus | Write Tree File in Nexus Format | |
| ape-internal | Internal Ape Functions | |
| as.alignment | Conversion Among DNA Sequence Internal Formats | |
| bird.families | Phylogeny of the Families of Birds From Sibley and Ahlquist | |
| DNAmodel | Defines Models of DNA Evolution | |
| bd.ext | Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates | |
| branching.times | Branching Times of a Phylogenetic Tree | |
| birthdeath | Estimation of Speciation and Extinction Rates With Birth-Death Models | |
| collapsed.intervals | Collapsed Coalescent Intervals | |
| corBlomberg | Blomberg et al.'s Correlation Structure | |
| corGrafen | Grafen's (1989) Correlation Structure | |
| compar.lynch | Lynch's Comparative Method | |
| dist.dna | Pairwise Distances from DNA Sequences | |
| diversi.time | Analysis of Diversification with Survival Models | |
| corMartins | Martins's (1997) Correlation Structure | |
| correlogram.formula | Phylogenetic Correlogram | |
| diversi.gof | Tests of Constant Diversification Rates | |
| read.dna | Read DNA Sequences in a File | |
| write.tree | Write Tree File in Parenthetic Format | |
| gammaStat | Gamma-Statistic of Pybus and Harvey | |
| drop.tip | Remove Tips in a Phylogenetic Tree | |
| yule | Fits Yule Model to a Phylogenetic Tree | |
| is.binary.tree | Test for Binary Tree | |
| howmanytrees | Calculate Numbers of Phylogenetic Trees | |
| read.nexus | Read Tree File in Nexus Format | |
| print.phylo | Compact Display of a Phylogeny | |
| reorder.phylo | Internal Reordering of Trees | |
| subtrees | All subtrees of a Phylogenetic Tree | |
| read.tree | Read Tree File in Parenthetic Format | |
| CADM.global | Congruence among distance matrices | |
| cophenetic.phylo | Pairwise Distances from a Phylogenetic Tree | |
| cherry | Number of Cherries and Null Models of Trees | |
| chiroptera | Bat Phylogeny | |
| mantel.test | Mantel Test for Similarity of Two Matrices | |
| dist.gene | Pairwise Distances from Genetic Data | |
| mcmc.popsize | Reversible Jump MCMC to Infer Demographic History | |
| nuc.div | Nucleotide Diversity | |
| yule.time | Fits the Time-Dependent Yule Model | |
| sh.test | Shimodaira-Hasegawa Test | |
| vcv.phylo | Phylogenetic Variance-covariance or Correlation Matrix | |
| rtree | Generates Random Trees | |
| as.phylo | Conversion Among Tree Objects | |
| as.matching | Conversion Between Phylo and Matching Objects | |
| carnivora | Carnivora body sizes and life history traits | |
| compute.brlen | Branch Lengths Computation | |
| evolve.phylo | Ancestral Character Simulation | |
| mat3 | Three Matrices | |
| makeNodeLabel | Makes Node Labels | |
| mlphylo | Estimating Phylogenies by Maximum Likelihood | |
| opsin | Gene Tree of 32 opsin Sequences | |
| pic | Phylogenetically Independent Contrasts | |
| yule.cov | Fits the Yule Model With Covariates | |
| seg.sites | Find Segregating Sites in DNA Sequences | |
| weight.taxo | Define Similarity Matrix | |
| No Results! | ||
Last month downloads
Details
| Date | 2009-09-09 |
| ZipData | no |
| License | GPL (>= 2) |
| URL | http://ape.mpl.ird.fr/ |
| Packaged | 2009-09-22 14:14:19 UTC; paradis |
| Repository | CRAN |
| Date/Publication | 2009-09-22 15:00:44 |
| depends | base (>= 2.6.0) , R (>= 2.6.0) |
| imports | gee , lattice , nlme |
| Contributors | Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Cuong, Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel, Christoph Heibl, Daniel Lawson, Vincent Lefort, Pierre Legendre, Jim Lemon, Yvonnick Noel, Johan Nylander, Rainer Opgen-Rhein, Korbinian Strimmer, Damien Vienne, Gangolf Jobb |
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