ape v3.0-9

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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, ancestral character analyses, analyses of diversification and macroevolution, computing distances from allelic and nucleotide data, reading and writing nucleotide sequences, and several tools such as Mantel's test, minimum spanning tree, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.

Functions in ape

Name Description
MPR Most Parsimonious Reconstruction
alex Alignment Explorer With Multiple Devices
as.phylo Conversion Among Tree and Network Objects
as.matching Conversion Between Phylo and Matching Objects
base.freq Base frequencies from DNA Sequences
branching.times Branching Times of a Phylogenetic Tree
c.phylo Building Lists of Trees
compute.brlen Branch Lengths Computation
corBlomberg Blomberg et al.'s Correlation Structure
additive Incomplete Distance Matrix Filling
balance Balance of a Dichotomous Phylogenetic Tree
corClasses Phylogenetic Correlation Structures
as.phylo.formula Conversion from Taxonomy Variables to Phylogenetic Trees
corBrownian Brownian Correlation Structure
compar.cheverud Cheverud's Comparative Method
edges Draw Additional Edges on a Plotted Tree
bird.orders Phylogeny of the Orders of Birds From Sibley and Ahlquist
mrca Find Most Recent Common Ancestors Between Pairs
evonet Evolutionary Networks
corGrafen Grafen's (1989) Correlation Structure
ladderize Ladderize a Tree
correlogram.formula Phylogenetic Correlogram
print.phylo Compact Display of a Phylogeny
DNAbin Manipulate DNA Sequences in Bit-Level Format
is.binary.tree Test for Binary Tree
howmanytrees Calculate Numbers of Phylogenetic Trees
mat5Mrand Five Independent Trees
gammaStat Gamma-Statistic of Pybus and Harvey
ewLasso Incomplete distances and edge weights of unrooted topology
bird.families Phylogeny of the Families of Birds From Sibley and Ahlquist
makeNodeLabel Makes Node Labels
BIONJ Tree Estimation Based on an Improved Version of the NJ Algorithm
identify.phylo Graphical Identification of Nodes and Tips
ape-package Analyses of Phylogenetics and Evolution
Initialize.corPhyl Initialize a `corPhyl' Structure Object
vcv Phylogenetic Variance-covariance or Correlation Matrix
CADM.global Congruence among distance matrices
mcconwaysims.test McConway-Sims Test of Homogeneous Diversification
landplants Gene Tree of 36 Landplant rbcL Sequences
varcomp Compute Variance Component Estimates
mat5M3ID Five Trees
dist.gene Pairwise Distances from Genetic Data
weight.taxo Define Similarity Matrix
as.bitsplits Conversion Among Split Classes
read.nexus Read Tree File in Nexus Format
data.nex NEXUS Data Example
rtree Generates Random Trees
image.DNAbin Plot of DNA Sequence Alignement
cophyloplot Plots two phylogenetic trees face to face with links between the tips.
clustal Multiple Sequence Alignment with External Applications
ape-internal Internal Ape Functions
speciesTree Species Tree Estimation
write.dna Write DNA Sequences in a File
varCompPhylip Variance Components with Orthonormal Contrasts
nj Neighbor-Joining Tree Estimation
mat3 Three Matrices
opsin Gene Tree of 32 opsin Sequences
skyline Skyline Plot Estimate of Effective Population Size
parafit Test of host-parasite coevolution
as.alignment Conversion Among DNA Sequence Internal Formats
add.scale.bar Add a Scale Bar to a Phylogeny Plot
carnivora Carnivora body sizes and life history traits
diversi.gof Tests of Constant Diversification Rates
corPagel Pagel's ``lambda'' Correlation Structure
bind.tree Binds Trees
coalescent.intervals Coalescent Intervals
seg.sites Find Segregating Sites in DNA Sequences
makeLabel Label Management
mixedFontLabel Mixed Font Labels for Plotting
pic Phylogenetically Independent Contrasts
mst Minimum Spanning Tree
slowinskiguyer.test Slowinski-Guyer Test of Homogeneous Diversification
plot.phylo Plot Phylogenies
is.ultrametric Test if a Tree is Ultrametric
delta.plot Delta Plots
trex Tree Explorer With Multiple Devices
rTraitMult Multivariate Character Simulation
unique.multiPhylo Revomes Duplicate Trees
mvr Minimum Variance Reduction
diversity.contrast.test Diversity Contrast Test
plot.correlogram Plot a Correlogram
treePop Tree Popping
lmorigin Multiple regression through the origin
bd.time Time-Dependent Birth-Death Models
Moran.I Moran's I Autocorrelation Index
phymltest Fits a Bunch of Models with PhyML
bd.ext Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
cophenetic.phylo Pairwise Distances from a Phylogenetic Tree
SDM Construction of Consensus Distance Matrix With SDM
axisPhylo Axis on Side of Phylogeny
mcmc.popsize Reversible Jump MCMC to Infer Demographic History
hivtree Phylogenetic Tree of 193 HIV-1 Sequences
subtreeplot Zoom on a Portion of a Phylogeny by Successive Clicks
nodelabels Labelling the Nodes, Tips, and Edges of a Tree
plot.varcomp Plot Variance Components
drop.tip Remove Tips in a Phylogenetic Tree
dist.dna Pairwise Distances from DNA Sequences
rlineage Tree Simulation Under the Time-Dependent Birth--Death Models
dbd Probability Density Under Birth--Death Models
birthdeath Estimation of Speciation and Extinction Rates With Birth-Death Models
pcoa Principal Coordinate Analysis
multiphylo Manipulating Lists of Trees
dist.topo Topological Distances Between Two Trees
read.dna Read DNA Sequences in a File
njs Tree Reconstruction from Incomplete Distances With NJ* or bio-NJ*
triangMtd Tree Reconstruction Based on the Triangles Method
pic.ortho Phylogenetically Independent Orthonormal Contrasts
read.caic Read Tree File in CAIC Format
rotate Swapping sister clades
rTraitDisc Discrete Character Simulation
root Roots Phylogenetic Trees
del.gaps Delete Alignment Gaps in DNA Sequences
corMartins Martins's (1997) Correlation Structure
is.monophyletic Is Group Monophyletic
multi2di Collapse and Resolve Multichotomies
stree Generates Systematic Regular Trees
read.GenBank Read DNA Sequences from GenBank via Internet
ace Ancestral Character Estimation
collapse.singles Collapse Single Nodes
is.compatible Check Compatibility of Splits
write.nexus Write Tree File in Nexus Format
chronopl Molecular Dating With Penalized Likelihood
which.edge Identifies Edges of a Tree
read.tree Read Tree File in Parenthetic Format
chiroptera Bat Phylogeny
woodmouse Cytochrome b Gene Sequences of Woodmice
write.nexus.data Write Character Data in NEXUS Format
yule Fits the Yule Model to a Phylogenetic Tree
yule.time Fits the Time-Dependent Yule Model
compar.ou Ornstein--Uhlenbeck Model for Continuous Characters
subtrees All subtrees of a Phylogenetic Tree
rTraitCont Continuous Character Simulation
richness.yule.test Test of Diversification-Shift With the Yule Process
boot.phylo Tree Bipartition and Bootstrapping Phylogenies
ltt.plot Lineages Through Time Plot
where Find Patterns in DNA Sequences
all.equal.phylo Global Comparison of two Phylogenies
kronoviz Plot Multiple Chronograms on the Same Scale
summary.phylo Print Summary of a Phylogeny
node.depth Depth and Heights of Nodes and Tips
matexpo Matrix Exponential
diversi.time Analysis of Diversification with Survival Models
reorder.phylo Internal Reordering of Trees
skylineplot Drawing Skyline Plot Graphs
FastME Tree Estimation Based on the Minimum Evolution Algorithm
compar.lynch Lynch's Comparative Method
read.nexus.data Read Character Data In NEXUS Format
compar.gee Comparative Analysis with GEEs
chronos Molecular Dating by Penalised Likelihood and Maximum Likelihood
chronoMPL Molecular Dating With Mean Path Lengths
yule.cov Fits the Yule Model With Covariates
compute.brtime Compute and Set Branching Times
consensus Concensus Trees
cherry Number of Cherries and Null Models of Trees
mantel.test Mantel Test for Similarity of Two Matrices
collapsed.intervals Collapsed Coalescent Intervals
write.tree Write Tree File in Parenthetic Format
zoom Zoom on a Portion of a Phylogeny
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Details

Date 2013-07-19
ZipData no
License GPL (>= 2)
URL http://ape-package.ird.fr/
Packaged 2013-07-19 13:20:48 UTC; paradis
NeedsCompilation yes
Repository CRAN
Date/Publication 2013-07-19 16:25:05

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