ape v2.5-1

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