ape v2.6-2

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