ape v2.1-2
0
Monthly downloads
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 | |
| ape-internal | Internal Ape Functions | |
| add.scale.bar | Add a Scale Bar to a Phylogeny Plot | |
| NPRS.criterion | Objective Function Employed in Nonparametric Rate Smoothing | |
| branching.times | Branching Times of a Phylogenetic Tree | |
| bird.families | Phylogeny of the Families of Birds From Sibley and Ahlquist | |
| balance | Balance of a Dichotomous Phylogenetic Tree | |
| compute.brlen | Branch Lengths Computation | |
| bind.tree | Binds Trees | |
| Moran.I | Moran's I Autocorrelation Index | |
| birthdeath | Estimation of Speciation and Extinction Rates With Birth-Death Models | |
| Initialize.corPhyl | Initialize a 'corPhyl' Structure Object | |
| bd.ext | Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates | |
| all.equal.phylo | Global Comparison of two Phylogenies | |
| carnivora | Carnivora body sizes and life history traits | |
| chiroptera | Bat Phylogeny | |
| compar.lynch | Lynch's Comparative Method | |
| heterozygosity | Heterozygosity at a Locus Using Gene Frequencies | |
| bird.orders | Phylogeny of the Orders of Birds From Sibley and Ahlquist | |
| as.matching | Conversion Between Phylo and Matching Objects | |
| chronogram | Chronogram Computed by Nonparametric Rate Smoothing | |
| diversi.gof | Tests of Constant Diversification Rates | |
| write.dna | Write DNA Sequences in a File | |
| phymltest | Fits a Bunch of Models with PHYML | |
| DNAmodel | Defines Models of DNA Evolution | |
| weight.taxo | Define Similarity Matrix | |
| chronoMPL | Molecular Dating With Mean Path Lengths | |
| as.phylo.formula | Conversion from Taxonomy Variables to Phylogenetic Trees | |
| FastME | Tree Estimation Based on the Minimum Evolution Algorithm | |
| cherry | Number of Cherries and Null Models of Trees | |
| BIONJ | Tree Estimation Based on an Improved Version of the NJ Algorithm | |
| as.alignment | Conversion Among DNA Sequence Internal Formats | |
| DNAbin | Manipulate DNA Sequences in Bit-Level Format | |
| ace | Ancestral Character Estimation | |
| hivtree | Phylogenetic Tree of 193 HIV-1 Sequences | |
| pic | Phylogenetically Independent Contrasts | |
| dist.dna | Pairwise Distances from DNA Sequences | |
| nj | Neighbor-Joining Tree Estimation | |
| corMartins | Martins's (1997) Correlation Structure | |
| rtree | Generates Random Trees | |
| consensus | Concensus Trees | |
| seg.sites | Find Segregating Sites in DNA Sequences | |
| boot.phylo | Tree Bipartition and Bootstrapping Phylogenies | |
| as.phylo | Conversion Among Tree Objects | |
| evolve.phylo | Ancestral Character Simulation | |
| read.dna | Read DNA Sequences in a File | |
| GC.content | Content in GC from DNA Sequences | |
| dist.gene | Pairwise Distances from Genetic Data | |
| compar.cheverud | Cheverud's Comparative Method | |
| axisPhylo | Axis on Side of Phylogeny | |
| base.freq | Base frequencies from DNA Sequences | |
| corGrafen | Grafen's (1989) Correlation Structure | |
| ltt.plot | Lineages Through Time Plot | |
| root | Roots Phylogenetic Trees | |
| mrca | Find Most Recent Common Ancestors Between Pairs | |
| skyline | Skyline Plot Estimate of Effective Population Size | |
| compar.gee | Comparative Analysis with GEEs | |
| corBrownian | Brownian Correlation Structure | |
| plot.correlogram | Plot a Correlogram | |
| collapse.singles | Collapse Single Nodes | |
| write.nexus | Write Tree File in Nexus Format | |
| yule | Fits Yule Model to a Phylogenetic Tree | |
| identify.phylo | Graphical Identification of Nodes and Tips | |
| dist.topo | Topological Distances Between Two Trees | |
| is.binary.tree | Test for Binary Tree | |
| theta.h | Population Parameter THETA using Homozygosity | |
| diversi.time | Analysis of Diversification with Survival Models | |
| cophenetic.phylo | Pairwise Distances from a Phylogenetic Tree | |
| coalescent.intervals | Coalescent Intervals | |
| read.caic | Read Tree File in CAIC Format | |
| matexpo | Matrix Exponential | |
| is.ultrametric | Test if a Tree is Ultrametric | |
| node.depth | Depth of Nodes and Tips | |
| drop.tip | Remove Tips in a Phylogenetic Tree | |
| mcmc.popsize | Reversible Jump MCMC to Infer Demographic History | |
| read.nexus.data | Read Character Data In NEXUS Format | |
| read.nexus | Read Tree File in Nexus Format | |
| opsin | Gene Tree of 32 opsin Sequences | |
| klastorin | Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000) | |
| reorder.phylo | Internal Reordering of Trees | |
| nuc.div | Nucleotide Diversity | |
| compar.ou | Ornstein--Uhlenbeck Model for Continuous Characters | |
| data.nex | NEXUS Data Example | |
| chronopl | Molecular Dating With Penalized Likelihood | |
| gammaStat | Gamma-Statistic of Pybus and Harvey | |
| write.nexus.data | Write Character Data In NEXUS Format | |
| print.phylo | Compact Display of a Phylogeny | |
| correlogram.formula | Phylogenetic Correlogram | |
| landplants | Gene Tree of 36 Landplant rbcL Sequences | |
| vcv.phylo | Phylogenetic Variance-covariance or Correlation Matrix | |
| collapsed.intervals | Collapsed Coalescent Intervals | |
| mst | Minimum Spanning Tree | |
| theta.k | Population Parameter THETA using Expected Number of Alleles | |
| howmanytrees | Calculate Numbers of Phylogenetic Trees | |
| mlphylo | Estimating Phylogenies by Maximum Likelihood | |
| woodmouse | Cytochrome b Gene Sequences of Woodmice | |
| ladderize | Ladderize a Tree | |
| corClasses | Phylogenetic Correlation Structures | |
| skylineplot | Drawing Skyline Plot Graphs | |
| read.tree | Read Tree File in Parenthetic Format | |
| plot.phylo | Plot Phylogenies | |
| rotate | Swopping sister clades | |
| mantel.test | Mantel Test for Similarity of Two Matrices | |
| multi2di | Collapse and Resolve Multichotomies | |
| plot.varcomp | Plot Variance Components | |
| ratogram | Ratogram Computed by Nonparametric Rate Smoothing | |
| write.tree | Write Tree File in Parenthetic Format | |
| xenarthra | Molecular Phylogeny of Living Xenarthrans | |
| unique.multiPhylo | Revomes Duplicate Trees | |
| plot.ancestral | Plot Ancestral Character Values on a Tree | |
| read.GenBank | Read DNA Sequences from GenBank via Internet | |
| theta.s | Population Parameter THETA using Segregating Sites in DNA Sequences | |
| summary.phylo | Print Summary of a Phylogeny | |
| varcomp | Compute Variance Component Estimates | |
| yule.cov | Fits the Yule Model With Covariates | |
| nodelabels | Labelling the Nodes, Tips, and Edges of a Tree | |
| sh.test | Shimodaira-Hasegawa Test | |
| zoom | Zoom on a Portion of a Phylogeny | |
| which.edge | Identifies Edges of a Tree | |
| No Results! | ||
Last month downloads
Details
| Date | 2008-02-28 |
| ZipData | no |
| License | GPL (>= 2) |
| URL | http://pbil.univ-lyon1.fr/R/ape/ |
| Packaged | Thu Feb 28 22:58:23 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 |
Include our badge in your README
[](http://www.rdocumentation.org/packages/ape)