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ape (version 5.1)

Analyses of Phylogenetics and Evolution

Description

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 DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, 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, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. 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.

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Version

Install

install.packages('ape')

Monthly Downloads

92,890

Version

5.1

License

GPL (>= 2)

Last Published

April 4th, 2018

Functions in ape (5.1)

alview

Print DNA or AA Sequence Alignement
axisPhylo

Axis on Side of Phylogeny
as.phylo

Conversion Among Tree and Network Objects
ape-package

Analyses of Phylogenetics and Evolution
as.phylo.formula

Conversion from Taxonomy Variables to Phylogenetic Trees
compar.cheverud

Cheverud's Comparative Method
BIONJ

Tree Estimation Based on an Improved Version of the NJ Algorithm
compar.gee

Comparative Analysis with GEEs
bind.tree

Binds Trees
bd.time

Time-Dependent Birth-Death Models
collapsed.intervals

Collapsed Coalescent Intervals
chiroptera

Bat Phylogeny
corBlomberg

Blomberg et al.'s Correlation Structure
compar.ou

Ornstein--Uhlenbeck Model for Continuous Characters
compar.lynch

Lynch's Comparative Method
chronoMPL

Molecular Dating With Mean Path Lengths
collapse.singles

Collapse Single Nodes
birthdeath

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

Phylogenetic Generalized Linear Mixed Model for Binary Data
boot.phylo

Tree Bipartition and Bootstrapping Phylogenies
balance

Balance of a Dichotomous Phylogenetic Tree
carnivora

Carnivora body sizes and life history traits
base.freq

Base frequencies from DNA Sequences
checkAlignment

Check DNA Alignments
as.bitsplits

Split Frequencies and Conversion Among Split Classes
corBrownian

Brownian Correlation Structure
bd.ext

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

Compare Two "phylo" Objects
chronos

Molecular Dating by Penalised Likelihood and Maximum Likelihood
compute.brlen

Branch Lengths Computation
gammaStat

Gamma-Statistic of Pybus and Harvey
chronopl

Molecular Dating With Penalized Likelihood
delta.plot

Delta Plots
ltt.plot

Lineages Through Time Plot
hivtree

Phylogenetic Tree of 193 HIV-1 Sequences
lmorigin

Multiple regression through the origin
mantel.test

Mantel Test for Similarity of Two Matrices
mat3

Three Matrices
dist.dna

Pairwise Distances from DNA Sequences
data.nex

NEXUS Data Example
corClasses

Phylogenetic Correlation Structures
branching.times

Branching Times of a Phylogenetic Tree
dbd

Probability Density Under Birth--Death Models
multi2di

Collapse and Resolve Multichotomies
diversity.contrast.test

Diversity Contrast Test
multiphylo

Manipulating Lists of Trees
as.matching

Conversion Between Phylo and Matching Objects
phydataplot

Tree Annotation
bird.families

Phylogeny of the Families of Birds From Sibley and Ahlquist
drop.tip

Remove Tips in a Phylogenetic Tree
pcoa

Principal Coordinate Analysis
corGrafen

Grafen's (1989) Correlation Structure
edges

Draw Additional Edges on a Plotted Tree
bird.orders

Phylogeny of the Orders of Birds From Sibley and Ahlquist
evonet

Evolutionary Networks
c.phylo

Building Lists of Trees
clustal

Multiple Sequence Alignment with External Applications
checkValidPhylo

Check the Structure of a "phylo" Object
is.compatible

Check Compatibility of Splits
coalescent.intervals

Coalescent Intervals
cherry

Number of Cherries and Null Models of Trees
compute.brtime

Compute and Set Branching Times
print.phylo

Compact Display of a Phylogeny
is.monophyletic

Is Group Monophyletic
matexpo

Matrix Exponential
rTraitCont

Continuous Character Simulation
trans

Translation from DNA to Amino Acid Sequences
root

Roots Phylogenetic Trees
rlineage

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

Concensus Trees
cophenetic.phylo

Pairwise Distances from a Phylogenetic Tree
treePop

Tree Popping
diversi.gof

Tests of Constant Diversification Rates
mcconwaysims.test

McConway-Sims Test of Homogeneous Diversification
corphylo

Correlations among Multiple Traits with Phylogenetic Signal
correlogram.formula

Phylogenetic Correlogram
del.gaps

Delete Alignment Gaps in DNA Sequences
def

Definition of Vectors for Plotting or Annotating
howmanytrees

Calculate Numbers of Phylogenetic Trees
cophyloplot

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

Graphical Identification of Nodes and Tips
makeLabel

Label Management
diversi.time

Analysis of Diversification with Survival Models
trex

Tree Explorer With Multiple Devices
njs

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

Zoom on a Portion of a Phylogeny
triangMtd

Tree Reconstruction Based on the Triangles Method
node.dating

node.dating
makeNodeLabel

Makes Node Labels
read.GenBank

Read DNA Sequences from GenBank via Internet
pic.ortho

Phylogenetically Independent Orthonormal Contrasts
plot.correlogram

Plot a Correlogram
ewLasso

Incomplete distances and edge weights of unrooted topology
read.caic

Read Tree File in CAIC Format
corMartins

Martins's (1997) Correlation Structure
FastME

Tree Estimation Based on the Minimum Evolution Algorithm
mcmc.popsize

Reversible Jump MCMC to Infer Demographic History
mixedFontLabel

Mixed Font Labels for Plotting
nodepath

Find Paths of Nodes
corPagel

Pagel's ``lambda'' Correlation Structure
is.ultrametric

Test if a Tree is Ultrametric
parafit

Test of host-parasite coevolution
plot.varcomp

Plot Variance Components
rotate

Swapping Sister Clades
plotTreeTime

Plot Tree With Time Axis
kronoviz

Plot Multiple Chronograms on the Same Scale
rtree

Generates Random Trees
mrca

Find Most Recent Common Ancestors Between Pairs
dist.gene

Pairwise Distances from Genetic Data
dist.topo

Topological Distances Between Two Trees
image.DNAbin

Plot of DNA Sequence Alignement
mst

Minimum Spanning Tree
read.dna

Read DNA Sequences in a File
read.gff

Read GFF Files
node.depth

Depth and Heights of Nodes and Tips
is.binary

Test for Binary Tree
nodelabels

Labelling the Nodes, Tips, and Edges of a Tree
read.tree

Read Tree File in Parenthetic Format
stree

Generates Systematic Regular Trees
label2table

Label Management
ladderize

Ladderize a Tree
plot.phylo

Plot Phylogenies
rTraitDisc

Discrete Character Simulation
rTraitMult

Multivariate Character Simulation
plot.phylo.extra

Extra Fuctions to Plot and Annotate Phylogenies
subtreeplot

Zoom on a Portion of a Phylogeny by Successive Clicks
reconstruct

Continuous Ancestral Character Estimation
subtrees

All subtrees of a Phylogenetic Tree
unique.multiPhylo

Revomes Duplicate Trees
rtt

Root a Tree by Root-to-Tip Regression
summary.phylo

Print Summary of a Phylogeny
seg.sites

Find Segregating Sites in DNA Sequences
mat5M3ID

Five Trees
mat5Mrand

Five Independent Trees
varCompPhylip

Variance Components with Orthonormal Contrasts
nj

Neighbor-Joining Tree Estimation
mvr

Minimum Variance Reduction
phymltest

Fits a Bunch of Models with PhyML
varcomp

Compute Variance Component Estimates
vcv

Phylogenetic Variance-covariance or Correlation Matrix
write.nexus

Write Tree File in Nexus Format
skyline

Skyline Plot Estimate of Effective Population Size
pic

Phylogenetically Independent Contrasts
skylineplot

Drawing Skyline Plot Graphs
write.nexus.data

Write Character Data in NEXUS Format
read.nexus

Read Tree File in Nexus Format
read.nexus.data

Read Character Data In NEXUS Format
where

Find Patterns in DNA Sequences
which.edge

Identifies Edges of a Tree
write.tree

Write Tree File in Parenthetic Format
reorder.phylo

Internal Reordering of Trees
yule.cov

Fits the Yule Model With Covariates
richness.yule.test

Test of Diversification-Shift With the Yule Process
yule

Fits the Yule Model to a Phylogenetic Tree
yule.time

Fits the Time-Dependent Yule Model
slowinskiguyer.test

Slowinski-Guyer Test of Homogeneous Diversification
speciesTree

Species Tree Estimation
vcv2phylo

Variance-Covariance Matrix to Tree
weight.taxo

Define Similarity Matrix
woodmouse

Cytochrome b Gene Sequences of Woodmice
write.dna

Write DNA Sequences in a File
SDM

Construction of Consensus Distance Matrix With SDM
alex

Alignment Explorer With Multiple Devices
ace

Ancestral Character Estimation
all.equal.DNAbin

Compare DNA Sets
Initialize.corPhyl

Initialize a `corPhyl' Structure Object
LTT

Theoretical Lineage-Through Time Plots
AAbin

Amino Acid Sequences
CADM.global

Congruence among distance matrices
MPR

Most Parsimonious Reconstruction
Moran.I

Moran's I Autocorrelation Index
all.equal.phylo

Global Comparison of two Phylogenies
apetools

Tools to Explore Files
add.scale.bar

Add a Scale Bar to a Phylogeny Plot
as.alignment

Conversion Among DNA Sequence Internal Formats
additive

Incomplete Distance Matrix Filling
DNAbin

Manipulate DNA Sequences in Bit-Level Format
DNAbin2indel

Recode Blocks of Indels
ape-internal

Internal Ape Functions