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ape (version 2.7-1)

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, 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

2.7-1

License

GPL (>= 2)

Maintainer

Emmanuel Paradis

Last Published

March 26th, 2011

Functions in ape (2.7-1)

cherry

Number of Cherries and Null Models of Trees
add.scale.bar

Add a Scale Bar to a Phylogeny Plot
GC.content

Content in GC from DNA Sequences
clustal

Multiple Sequence Alignment with External Applications
ape-internal

Internal Ape Functions
collapse.singles

Collapse Single Nodes
corClasses

Phylogenetic Correlation Structures
birthdeath

Estimation of Speciation and Extinction Rates With Birth-Death Models
DNAbin

Manipulate DNA Sequences in Bit-Level Format
chronoMPL

Molecular Dating With Mean Path Lengths
c.phylo

Building Lists of Trees
identify.phylo

Graphical Identification of Nodes and Tips
corGrafen

Grafen's (1989) Correlation Structure
mst

Minimum Spanning Tree
as.phylo

Conversion Among Tree and Network Objects
coalescent.intervals

Coalescent Intervals
balance

Balance of a Dichotomous Phylogenetic Tree
Moran.I

Moran's I Autocorrelation Index
base.freq

Base frequencies from DNA Sequences
BIONJ

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

Blomberg et al.'s Correlation Structure
CADM.global

Congruence among distance matrices
as.alignment

Conversion Among DNA Sequence Internal Formats
as.matching

Conversion Between Phylo and Matching Objects
edges

Draw Additional Edges on a Plotted Tree
chronopl

Molecular Dating With Penalized Likelihood
compar.ou

Ornstein--Uhlenbeck Model for Continuous Characters
chiroptera

Bat Phylogeny
as.phylo.formula

Conversion from Taxonomy Variables to Phylogenetic Trees
cophenetic.phylo

Pairwise Distances from a Phylogenetic Tree
summary.phylo

Print Summary of a Phylogeny
corPagel

Pagel's ``lambda'' Correlation Structure
collapsed.intervals

Collapsed Coalescent Intervals
ape-defunct

Defunct Ape Functions
consensus

Concensus Trees
Initialize.corPhyl

Initialize a `corPhyl' Structure Object
carnivora

Carnivora body sizes and life history traits
lmorigin

Multiple regression through the origin
correlogram.formula

Phylogenetic Correlogram
compute.brlen

Branch Lengths Computation
bird.orders

Phylogeny of the Orders of Birds From Sibley and Ahlquist
corBrownian

Brownian Correlation Structure
boot.phylo

Tree Bipartition and Bootstrapping Phylogenies
bd.time

Time-Dependent Birth-Death Models
ace

Ancestral Character Estimation
nj

Neighbor-Joining Tree Estimation
write.nexus

Write Tree File in Nexus Format
bind.tree

Binds Trees
del.gaps

Delete Alignment Gaps in DNA Sequences
compar.cheverud

Cheverud's Comparative Method
write.tree

Write Tree File in Parenthetic Format
dist.dna

Pairwise Distances from DNA Sequences
pic

Phylogenetically Independent Contrasts
FastME

Tree Estimation Based on the Minimum Evolution Algorithm
bird.families

Phylogeny of the Families of Birds From Sibley and Ahlquist
dist.gene

Pairwise Distances from Genetic Data
dist.topo

Topological Distances Between Two Trees
diversity.contrast.test

Diversity Contrast Test
compar.gee

Comparative Analysis with GEEs
landplants

Gene Tree of 36 Landplant rbcL Sequences
drop.tip

Remove Tips in a Phylogenetic Tree
kronoviz

Plot Multiple Chronograms on the Same Scale
makeNodeLabel

Makes Node Labels
write.dna

Write DNA Sequences in a File
mantel.test

Mantel Test for Similarity of Two Matrices
diversi.time

Analysis of Diversification with Survival Models
opsin

Gene Tree of 32 opsin Sequences
nodelabels

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

Matrix Exponential
plot.correlogram

Plot a Correlogram
cophyloplot

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

Fits a Bunch of Models with PhyML
parafit

Test of host-parasite coevolution
makeLabel

Label Management
read.nexus.data

Read Character Data In NEXUS Format
ladderize

Ladderize a Tree
yule.cov

Fits the Yule Model With Covariates
which.edge

Identifies Edges of a Tree
all.equal.phylo

Global Comparison of two Phylogenies
weight.taxo

Define Similarity Matrix
is.monophyletic

Is Group Monophyletic
delta.plot

Delta Plots
ltt.plot

Lineages Through Time Plot
image.DNAbin

Plot of DNA Sequence Alignement
mat5M3ID

Five Trees
hivtree

Phylogenetic Tree of 193 HIV-1 Sequences
multiphylo

Manipulating Lists of Trees
rTraitCont

Continuous Character Simulation
subtreeplot

Zoom on a Portion of a Phylogeny by Successive Clicks
multi2di

Collapse and Resolve Multichotomies
unique.multiPhylo

Revomes Duplicate Trees
zoom

Zoom on a Portion of a Phylogeny
plot.phylo

Plot Phylogenies
speciesTree

Species Tree Estimation
corMartins

Martins's (1997) Correlation Structure
is.binary.tree

Test for Binary Tree
mrca

Find Most Recent Common Ancestors Between Pairs
is.ultrametric

Test if a Tree is Ultrametric
data.nex

NEXUS Data Example
ape-package

Analyses of Phylogenetics and Evolution
stree

Generates Systematic Regular Trees
root

Roots Phylogenetic Trees
read.dna

Read DNA Sequences in a File
write.nexus.data

Write Character Data In NEXUS Format
read.nexus

Read Tree File in Nexus Format
skylineplot

Drawing Skyline Plot Graphs
read.tree

Read Tree File in Parenthetic Format
pic.ortho

Phylogenetically Independent Orthonormal Contrasts
mat3

Three Matrices
slowinskiguyer.test

Slowinski-Guyer Test of Homogeneous Diversification
plot.varcomp

Plot Variance Components
reorder.phylo

Internal Reordering of Trees
rTraitDisc

Discrete Character Simulation
mcconwaysims.test

McConway-Sims Test of Homogeneous Diversification
diversi.gof

Tests of Constant Diversification Rates
gammaStat

Gamma-Statistic of Pybus and Harvey
read.caic

Read Tree File in CAIC Format
yule.time

Fits the Time-Dependent Yule Model
rtree

Generates Random Trees
subtrees

All subtrees of a Phylogenetic Tree
yule

Fits Yule Model to a Phylogenetic Tree
pcoa

Principal Coordinate Analysis
skyline

Skyline Plot Estimate of Effective Population Size
trex

Tree Explorer With Multiple Devices
woodmouse

Cytochrome b Gene Sequences of Woodmice
varCompPhylip

Variance Components with Orthonormal Contrasts
branching.times

Branching Times of a Phylogenetic Tree
mcmc.popsize

Reversible Jump MCMC to Infer Demographic History
print.phylo

Compact Display of a Phylogeny
seg.sites

Find Segregating Sites in DNA Sequences
MPR

Most Parsimonious Reconstruction
varcomp

Compute Variance Component Estimates
richness.yule.test

Test of Diversification-Shift With the Yule Process
bd.ext

Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
compar.lynch

Lynch's Comparative Method
howmanytrees

Calculate Numbers of Phylogenetic Trees
mat5Mrand

Five Independent Trees
mixedFontLabel

Mixed Font Labels for Plotting
vcv

Phylogenetic Variance-covariance or Correlation Matrix
axisPhylo

Axis on Side of Phylogeny
node.depth

Depth of Nodes and Tips
read.GenBank

Read DNA Sequences from GenBank via Internet
rotate

Swapping sister clades
rlineage

Tree Simulation Under the Time-Dependent Birth--Death Models
evonet

Evolutionary Networks
rTraitMult

Multivariate Character Simulation
compute.brtime

Compute and Set Branching Times