ape v2.5-2

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