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ape (version 2.3-3)

Analyses of Phylogenetics and Evolution

Description

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. Phylogeny estimation can be done with the NJ, BIONJ, and ME methods.

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Version

Install

install.packages('ape')

Monthly Downloads

87,302

Version

2.3-3

License

GPL (>= 2)

Maintainer

Emmanuel Paradis

Last Published

September 22nd, 2009

Functions in ape (2.3-3)

DNAbin

Manipulate DNA Sequences in Bit-Level Format
compar.gee

Comparative Analysis with GEEs
bird.orders

Phylogeny of the Orders of Birds From Sibley and Ahlquist
heterozygosity

Heterozygosity at a Locus Using Gene Frequencies
landplants

Gene Tree of 36 Landplant rbcL Sequences
ltt.plot

Lineages Through Time Plot
BIONJ

Tree Estimation Based on an Improved Version of the NJ Algorithm
matexpo

Matrix Exponential
plot.correlogram

Plot a Correlogram
balance

Balance of a Dichotomous Phylogenetic Tree
base.freq

Base frequencies from DNA Sequences
read.GenBank

Read DNA Sequences from GenBank via Internet
GC.content

Content in GC from DNA Sequences
chronogram

Chronogram Computed by Nonparametric Rate Smoothing
chronoMPL

Molecular Dating With Mean Path Lengths
coalescent.intervals

Coalescent Intervals
theta.h

Population Parameter THETA using Homozygosity
add.scale.bar

Add a Scale Bar to a Phylogeny Plot
all.equal.phylo

Global Comparison of two Phylogenies
bind.tree

Binds Trees
boot.phylo

Tree Bipartition and Bootstrapping Phylogenies
data.nex

NEXUS Data Example
Initialize.corPhyl

Initialize a `corPhyl' Structure Object
is.ultrametric

Test if a Tree is Ultrametric
Moran.I

Moran's I Autocorrelation Index
ace

Ancestral Character Estimation
makeLabel

Label Management
compar.cheverud

Cheverud's Comparative Method
NPRS.criterion

Objective Function Employed in Nonparametric Rate Smoothing
collapse.singles

Collapse Single Nodes
ladderize

Ladderize a Tree
ape-package

Analyses of Phylogenetics and Evolution
compar.ou

Ornstein--Uhlenbeck Model for Continuous Characters
hivtree

Phylogenetic Tree of 193 HIV-1 Sequences
cophyloplot

Plots two phylogenetic trees face to face with links between the tips.
identify.phylo

Graphical Identification of Nodes and Tips
FastME

Tree Estimation Based on the Minimum Evolution Algorithm
corBrownian

Brownian Correlation Structure
mst

Minimum Spanning Tree
is.monophyletic

Is Group Monophyletic
mrca

Find Most Recent Common Ancestors Between Pairs
nodelabels

Labelling the Nodes, Tips, and Edges of a Tree
consensus

Concensus Trees
mat5M3ID

Five Trees
read.caic

Read Tree File in CAIC Format
read.nexus.data

Read Character Data In NEXUS Format
node.depth

Depth of Nodes and Tips
plot.ancestral

Plot Ancestral Character Values on a Tree
as.phylo.formula

Conversion from Taxonomy Variables to Phylogenetic Trees
dist.topo

Topological Distances Between Two Trees
skylineplot

Drawing Skyline Plot Graphs
axisPhylo

Axis on Side of Phylogeny
unique.multiPhylo

Revomes Duplicate Trees
chronopl

Molecular Dating With Penalized Likelihood
nj

Neighbor-Joining Tree Estimation
plot.varcomp

Plot Variance Components
varcomp

Compute Variance Component Estimates
ratogram

Ratogram Computed by Nonparametric Rate Smoothing
which.edge

Identifies Edges of a Tree
woodmouse

Cytochrome b Gene Sequences of Woodmice
corPagel

Pagel's ``lambda'' Correlation Structure
write.nexus.data

Write Character Data In NEXUS Format
plot.phylo

Plot Phylogenies
write.dna

Write DNA Sequences in a File
zoom

Zoom on a Portion of a Phylogeny
summary.phylo

Print Summary of a Phylogeny
corClasses

Phylogenetic Correlation Structures
theta.s

Population Parameter THETA using Segregating Sites in DNA Sequences
subtreeplot

Zoom on a Portion of a Phylogeny by Successive Clicks
del.gaps

Delete Alignment Gaps in DNA Sequences
phymltest

Fits a Bunch of Models with PhyML
multi2di

Collapse and Resolve Multichotomies
root

Roots Phylogenetic Trees
skyline

Skyline Plot Estimate of Effective Population Size
mat5Mrand

Five Independent Trees
rotate

Swapping sister clades
theta.k

Population Parameter THETA using Expected Number of Alleles
write.nexus

Write Tree File in Nexus Format
ape-internal

Internal Ape Functions
as.alignment

Conversion Among DNA Sequence Internal Formats
bird.families

Phylogeny of the Families of Birds From Sibley and Ahlquist
DNAmodel

Defines Models of DNA Evolution
bd.ext

Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
branching.times

Branching Times of a Phylogenetic Tree
birthdeath

Estimation of Speciation and Extinction Rates With Birth-Death Models
collapsed.intervals

Collapsed Coalescent Intervals
corBlomberg

Blomberg et al.'s Correlation Structure
corGrafen

Grafen's (1989) Correlation Structure
compar.lynch

Lynch's Comparative Method
dist.dna

Pairwise Distances from DNA Sequences
diversi.time

Analysis of Diversification with Survival Models
corMartins

Martins's (1997) Correlation Structure
correlogram.formula

Phylogenetic Correlogram
diversi.gof

Tests of Constant Diversification Rates
read.dna

Read DNA Sequences in a File
write.tree

Write Tree File in Parenthetic Format
gammaStat

Gamma-Statistic of Pybus and Harvey
drop.tip

Remove Tips in a Phylogenetic Tree
yule

Fits Yule Model to a Phylogenetic Tree
is.binary.tree

Test for Binary Tree
howmanytrees

Calculate Numbers of Phylogenetic Trees
read.nexus

Read Tree File in Nexus Format
print.phylo

Compact Display of a Phylogeny
reorder.phylo

Internal Reordering of Trees
subtrees

All subtrees of a Phylogenetic Tree
read.tree

Read Tree File in Parenthetic Format
CADM.global

Congruence among distance matrices
cophenetic.phylo

Pairwise Distances from a Phylogenetic Tree
cherry

Number of Cherries and Null Models of Trees
chiroptera

Bat Phylogeny
mantel.test

Mantel Test for Similarity of Two Matrices
dist.gene

Pairwise Distances from Genetic Data
mcmc.popsize

Reversible Jump MCMC to Infer Demographic History
nuc.div

Nucleotide Diversity
yule.time

Fits the Time-Dependent Yule Model
sh.test

Shimodaira-Hasegawa Test
vcv.phylo

Phylogenetic Variance-covariance or Correlation Matrix
rtree

Generates Random Trees
as.phylo

Conversion Among Tree Objects
as.matching

Conversion Between Phylo and Matching Objects
carnivora

Carnivora body sizes and life history traits
compute.brlen

Branch Lengths Computation
evolve.phylo

Ancestral Character Simulation
mat3

Three Matrices
makeNodeLabel

Makes Node Labels
mlphylo

Estimating Phylogenies by Maximum Likelihood
opsin

Gene Tree of 32 opsin Sequences
pic

Phylogenetically Independent Contrasts
yule.cov

Fits the Yule Model With Covariates
seg.sites

Find Segregating Sites in DNA Sequences
weight.taxo

Define Similarity Matrix