Learn R Programming

⚠️There's a newer version (5.8-1) of this package.Take me there.

ape (version 3.0-4)

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, ancestral character analyses, analyses of diversification and macroevolution, computing distances from allelic and nucleotide data, reading and writing nucleotide sequences, and several tools such as Mantel's test, minimum spanning tree, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.

Copy Link

Version

Install

install.packages('ape')

Monthly Downloads

87,302

Version

3.0-4

License

GPL (>= 2)

Maintainer

Emmanuel Paradis

Last Published

August 1st, 2012

Functions in ape (3.0-4)

as.phylo.formula

Conversion from Taxonomy Variables to Phylogenetic Trees
clustal

Multiple Sequence Alignment with External Applications
Moran.I

Moran's I Autocorrelation Index
additive

Incomplete Distance Matrix Filling
MPR

Most Parsimonious Reconstruction
corClasses

Phylogenetic Correlation Structures
all.equal.phylo

Global Comparison of two Phylogenies
add.scale.bar

Add a Scale Bar to a Phylogeny Plot
cherry

Number of Cherries and Null Models of Trees
c.phylo

Building Lists of Trees
balance

Balance of a Dichotomous Phylogenetic Tree
as.alignment

Conversion Among DNA Sequence Internal Formats
as.bitsplits

Conversion Among Split Classes
ape-internal

Internal Ape Functions
axisPhylo

Axis on Side of Phylogeny
compar.ou

Ornstein--Uhlenbeck Model for Continuous Characters
pic.ortho

Phylogenetically Independent Orthonormal Contrasts
coalescent.intervals

Coalescent Intervals
rTraitCont

Continuous Character Simulation
consensus

Concensus Trees
bd.ext

Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
DNAbin

Manipulate DNA Sequences in Bit-Level Format
identify.phylo

Graphical Identification of Nodes and Tips
CADM.global

Congruence among distance matrices
edges

Draw Additional Edges on a Plotted Tree
multiphylo

Manipulating Lists of Trees
bd.time

Time-Dependent Birth-Death Models
mvr

Minimum Variance Reduction
rTraitDisc

Discrete Character Simulation
which.edge

Identifies Edges of a Tree
print.phylo

Compact Display of a Phylogeny
read.nexus.data

Read Character Data In NEXUS Format
reorder.phylo

Internal Reordering of Trees
mcconwaysims.test

McConway-Sims Test of Homogeneous Diversification
mst

Minimum Spanning Tree
opsin

Gene Tree of 32 opsin Sequences
write.tree

Write Tree File in Parenthetic Format
rotate

Swapping sister clades
plot.varcomp

Plot Variance Components
unique.multiPhylo

Revomes Duplicate Trees
is.compatible

Check Compatibility of Splits
seg.sites

Find Segregating Sites in DNA Sequences
collapsed.intervals

Collapsed Coalescent Intervals
rlineage

Tree Simulation Under the Time-Dependent Birth--Death Models
ape-package

Analyses of Phylogenetics and Evolution
speciesTree

Species Tree Estimation
makeNodeLabel

Makes Node Labels
Initialize.corPhyl

Initialize a `corPhyl' Structure Object
nj

Neighbor-Joining Tree Estimation
mat5Mrand

Five Independent Trees
cophenetic.phylo

Pairwise Distances from a Phylogenetic Tree
pcoa

Principal Coordinate Analysis
read.nexus

Read Tree File in Nexus Format
trex

Tree Explorer With Multiple Devices
mat5M3ID

Five Trees
read.tree

Read Tree File in Parenthetic Format
base.freq

Base frequencies from DNA Sequences
hivtree

Phylogenetic Tree of 193 HIV-1 Sequences
read.caic

Read Tree File in CAIC Format
cophyloplot

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

Bat Phylogeny
mat3

Three Matrices
bind.tree

Binds Trees
SDM

Construction of Consensus Distance Matrix With SDM
mrca

Find Most Recent Common Ancestors Between Pairs
carnivora

Carnivora body sizes and life history traits
summary.phylo

Print Summary of a Phylogeny
dist.gene

Pairwise Distances from Genetic Data
matexpo

Matrix Exponential
read.GenBank

Read DNA Sequences from GenBank via Internet
compar.cheverud

Cheverud's Comparative Method
diversi.gof

Tests of Constant Diversification Rates
varCompPhylip

Variance Components with Orthonormal Contrasts
corGrafen

Grafen's (1989) Correlation Structure
bird.families

Phylogeny of the Families of Birds From Sibley and Ahlquist
varcomp

Compute Variance Component Estimates
weight.taxo

Define Similarity Matrix
write.nexus.data

Write Character Data In NEXUS Format
compar.lynch

Lynch's Comparative Method
kronoviz

Plot Multiple Chronograms on the Same Scale
yule.time

Fits the Time-Dependent Yule Model
woodmouse

Cytochrome b Gene Sequences of Woodmice
zoom

Zoom on a Portion of a Phylogeny
delta.plot

Delta Plots
image.DNAbin

Plot of DNA Sequence Alignement
nodelabels

Labelling the Nodes, Tips, and Edges of a Tree
correlogram.formula

Phylogenetic Correlogram
parafit

Test of host-parasite coevolution
birthdeath

Estimation of Speciation and Extinction Rates With Birth-Death Models
data.nex

NEXUS Data Example
gammaStat

Gamma-Statistic of Pybus and Harvey
pic

Phylogenetically Independent Contrasts
as.matching

Conversion Between Phylo and Matching Objects
corBlomberg

Blomberg et al.'s Correlation Structure
is.monophyletic

Is Group Monophyletic
subtreeplot

Zoom on a Portion of a Phylogeny by Successive Clicks
chronoMPL

Molecular Dating With Mean Path Lengths
bird.orders

Phylogeny of the Orders of Birds From Sibley and Ahlquist
multi2di

Collapse and Resolve Multichotomies
alex

Alignment Explorer With Multiple Devices
branching.times

Branching Times of a Phylogenetic Tree
plot.correlogram

Plot a Correlogram
BIONJ

Tree Estimation Based on an Improved Version of the NJ Algorithm
write.dna

Write DNA Sequences in a File
root

Roots Phylogenetic Trees
rTraitMult

Multivariate Character Simulation
vcv

Phylogenetic Variance-covariance or Correlation Matrix
collapse.singles

Collapse Single Nodes
mixedFontLabel

Mixed Font Labels for Plotting
dbd

Probability Density Under Birth--Death Models
stree

Generates Systematic Regular Trees
triangMtd

Tree Reconstruction Based on the Triangles Method
ladderize

Ladderize a Tree
mcmc.popsize

Reversible Jump MCMC to Infer Demographic History
phymltest

Fits a Bunch of Models with PhyML
richness.yule.test

Test of Diversification-Shift With the Yule Process
drop.tip

Remove Tips in a Phylogenetic Tree
read.dna

Read DNA Sequences in a File
corBrownian

Brownian Correlation Structure
is.ultrametric

Test if a Tree is Ultrametric
node.depth

Depth of Nodes and Tips
njs

Tree Reconstruction from Incomplete Distances With NJ* or bio-NJ*
subtrees

All subtrees of a Phylogenetic Tree
plot.phylo

Plot Phylogenies
treePop

Tree Popping
ace

Ancestral Character Estimation
yule

Fits the Yule Model to a Phylogenetic Tree
write.nexus

Write Tree File in Nexus Format
yule.cov

Fits the Yule Model With Covariates
chronopl

Molecular Dating With Penalized Likelihood
ltt.plot

Lineages Through Time Plot
skyline

Skyline Plot Estimate of Effective Population Size
mantel.test

Mantel Test for Similarity of Two Matrices
slowinskiguyer.test

Slowinski-Guyer Test of Homogeneous Diversification
rtree

Generates Random Trees
boot.phylo

Tree Bipartition and Bootstrapping Phylogenies
compute.brtime

Compute and Set Branching Times
landplants

Gene Tree of 36 Landplant rbcL Sequences
compar.gee

Comparative Analysis with GEEs
makeLabel

Label Management
compute.brlen

Branch Lengths Computation
skylineplot

Drawing Skyline Plot Graphs
as.phylo

Conversion Among Tree and Network Objects
del.gaps

Delete Alignment Gaps in DNA Sequences
is.binary.tree

Test for Binary Tree
howmanytrees

Calculate Numbers of Phylogenetic Trees
diversi.time

Analysis of Diversification with Survival Models
corMartins

Martins's (1997) Correlation Structure
lmorigin

Multiple regression through the origin
evonet

Evolutionary Networks
diversity.contrast.test

Diversity Contrast Test
FastME

Tree Estimation Based on the Minimum Evolution Algorithm
dist.topo

Topological Distances Between Two Trees
dist.dna

Pairwise Distances from DNA Sequences
corPagel

Pagel's ``lambda'' Correlation Structure