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install.packages('ape')

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92,890

Version

5.8

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GPL-2 | GPL-3

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Last Published

April 11th, 2024

Functions in ape (5.8)

SDM

Construction of Consensus Distance Matrix With SDM
AAbin

Amino Acid Sequences
CADM.global

Congruence among distance matrices
ace

Ancestral Character Estimation
Initialize.corPhyl

Initialize a `corPhyl' Structure Object
all.equal.phylo

Global Comparison of two Phylogenies
alview

Print DNA or AA Sequence Alignement
DNAbin

Manipulate DNA Sequences in Bit-Level Format
DNAbin2indel

Recode Blocks of Indels
bd.time

Time-Dependent Birth-Death Models
apetools

Tools to Explore Files
alex

Alignment Explorer With Multiple Devices
binaryPGLMM

Phylogenetic Generalized Linear Mixed Model for Binary Data
as.alignment

Conversion Among DNA Sequence Internal Formats
base.freq

Base frequencies from DNA Sequences
LTT

Theoretical Lineage-Through Time Plots
ape-internal

Internal Ape Functions
ape-package

Analyses of Phylogenetics and Evolution
bd.ext

Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
bird.families

Phylogeny of the Families of Birds From Sibley and Ahlquist
carnivora

Carnivora body sizes and life history traits
bird.orders

Phylogeny of the Orders of Birds From Sibley and Ahlquist
checkAlignment

Check DNA Alignments
MPR

Most Parsimonious Reconstruction
chronoMPL

Molecular Dating With Mean Path Lengths
chronopl

Molecular Dating With Penalized Likelihood
checkLabel

Checking Labels
compar.ou

Ornstein--Uhlenbeck Model for Continuous Characters
comparePhylo

Compare Two "phylo" Objects
Moran.I

Moran's I Autocorrelation Index
checkValidPhylo

Check the Structure of a "phylo" Object
cophyloplot

Plots two phylogenetic trees face to face with links between the tips.
add.scale.bar

Add a Scale Bar to a Phylogeny Plot
compute.brlen

Branch Lengths Computation
corBlomberg

Blomberg et al.'s Correlation Structure
all.equal.DNAbin

Compare DNA Sets
delta.plot

Delta Plots
compute.brtime

Compute and Set Branching Times
corPagel

Pagel's ``lambda'' Correlation Structure
corphylo

Correlations among Multiple Traits with Phylogenetic Signal
as.phylo

Conversion Among Tree and Network Objects
diversi.gof

Tests of Constant Diversification Rates
additive

Incomplete Distance Matrix Filling
dist.dna

Pairwise Distances from DNA Sequences
getAnnotationsGenBank

Read Annotations from GenBank
axisPhylo

Axis on Side of Phylogeny
as.bitsplits

Split Frequencies and Conversion Among Split Classes
diversi.time

Analysis of Diversification with Survival Models
balance

Balance of a Dichotomous Phylogenetic Tree
hivtree

Phylogenetic Tree of 193 HIV-1 Sequences
label2table

Label Management
as.matching

Conversion Between Phylo and Matching Objects
as.phylo.formula

Conversion from Taxonomy Variables to Phylogenetic Trees
ladderize

Ladderize a Tree
bind.tree

Binds Trees
birthdeath

Estimation of Speciation and Extinction Rates With Birth-Death Models
ltt.plot

Lineages Through Time Plot
boot.phylo

Tree Bipartition and Bootstrapping Phylogenies
drop.tip

Remove Tips in a Phylogenetic Tree
makeLabel

Label Management
edges

Draw Additional Edges on a Plotted Tree
chronos

Molecular Dating by Penalised Likelihood and Maximum Likelihood
image.DNAbin

Plot of DNA Sequence Alignement
is.binary

Test for Binary Tree
latag2n

Leading and Trailing Alignment Gaps to N
BIONJ

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

Mixed Font Labels for Plotting
coalescent.intervals

Coalescent Intervals
clustal

Multiple Sequence Alignment with External Applications
mrca

Find Most Recent Common Ancestors Between Pairs
branching.times

Branching Times of a Phylogenetic Tree
collapse.singles

Collapse Single Nodes
compar.gee

Comparative Analysis with GEEs
pic

Phylogenetically Independent Contrasts
compar.lynch

Lynch's Comparative Method
corGrafen

Grafen's (1989) Correlation Structure
lmorigin

Multiple regression through the origin
corMartins

Martins's (1997) Correlation Structure
collapsed.intervals

Collapsed Coalescent Intervals
compar.cheverud

Cheverud's Comparative Method
correlogram.formula

Phylogenetic Correlogram
degree

Vertex Degrees in Trees and Networks
data.nex

NEXUS Data Example
pic.ortho

Phylogenetically Independent Orthonormal Contrasts
c.phylo

Building Lists of Trees
dbd

Probability Density Under Birth--Death Models
cherry

Number of Cherries and Null Models of Trees
chiroptera

Bat Phylogeny
plotTreeTime

Plot Tree With Time Axis
def

Definition of Vectors for Plotting or Annotating
print.phylo

Compact Display of a Phylogeny
nj

Neighbor-Joining Tree Estimation
del.gaps

Delete Alignment Gaps in DNA or AA Sequences
FastME

Tree Estimation Based on the Minimum Evolution Algorithm
njs

Tree Reconstruction from Incomplete Distances With NJ* or bio-NJ*
diversity.contrast.test

Diversity Contrast Test
dnds

dN/dS Ratio
gammaStat

Gamma-Statistic of Pybus and Harvey
nodelabels

Labelling the Nodes, Tips, and Edges of a Tree
is.compatible

Check Compatibility of Splits
howmanytrees

Calculate Numbers of Phylogenetic Trees
identify.phylo

Graphical Identification of Nodes and Tips
nodepath

Find Paths of Nodes
is.monophyletic

Is Group Monophyletic
plot.phylo.extra

Extra Fuctions to Plot and Annotate Phylogenies
plot.varcomp

Plot Variance Components
makeNodeLabel

Makes Node Labels
read.GenBank

Read DNA Sequences from GenBank via Internet
read.caic

Read Tree File in CAIC Format
reorder.phylo

Internal Reordering of Trees
mat3

Three Matrices
mantel.test

Mantel Test for Similarity of Two Matrices
mst

Minimum Spanning Tree
richness.yule.test

Test of Diversification-Shift With the Yule Process
multi2di

Collapse and Resolve Multichotomies
consensus

Concensus Trees
mat5M3ID

Five Trees
cophenetic.phylo

Pairwise Distances from a Phylogenetic Tree
corBrownian

Brownian Correlation Structure
parafit

Test of host-parasite coevolution
corClasses

Phylogenetic Correlation Structures
pcoa

Principal Coordinate Analysis
dist.gene

Pairwise Distances from Genetic Data
skyline

Skyline Plot Estimate of Effective Population Size
mcconwaysims.test

McConway-Sims Test of Homogeneous Diversification
mcmc.popsize

Reversible Jump MCMC to Infer Demographic History
skylineplot

Drawing Skyline Plot Graphs
dist.topo

Topological Distances Between Two Trees
evonet

Evolutionary Networks
ewLasso

Incomplete distances and edge weights of unrooted topology
node.dating

node.dating
is.ultrametric

Test if a Tree is Ultrametric
subtreeplot

Zoom on a Portion of a Phylogeny by Successive Clicks
subtrees

All subtrees of a Phylogenetic Tree
node.depth

Depth and Heights of Nodes and Tips
rlineage

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

Roots Phylogenetic Trees
rTraitDisc

Discrete Character Simulation
rDNAbin

Random DNA Sequences
kronoviz

Plot Multiple Chronograms on the Same Scale
rTraitCont

Continuous Character Simulation
rTraitMult

Multivariate Character Simulation
updateLabel

Update Labels
read.nexus

Read Tree File in Nexus Format
read.nexus.data

Read Character Data In NEXUS Format
mat5Mrand

Five Independent Trees
varCompPhylip

Variance Components with Orthonormal Contrasts
rtt

Root a Tree by Root-to-Tip Regression
read.dna

Read DNA Sequences in a File
read.gff

Read GFF Files
treePop

Tree Popping
matexpo

Matrix Exponential
multiphylo

Manipulating Lists of Trees
trex

Tree Explorer With Multiple Devices
seg.sites

Find Segregating Sites in DNA Sequences
mvr

Minimum Variance Reduction
phydataplot

Tree Annotation
slowinskiguyer.test

Slowinski-Guyer Test of Homogeneous Diversification
solveAmbiguousBases

Solve Ambiguous Bases in DNA Sequences
speciesTree

Species Tree Estimation
stree

Generates Systematic Regular Trees
woodmouse

Cytochrome b Gene Sequences of Woodmice
write.dna

Write DNA Sequences in a File
phymltest

Fits a Bunch of Models with PhyML
write.nexus

Write Tree File in Nexus Format
plot.correlogram

Plot a Correlogram
summary.phylo

Print Summary of a Phylogeny
plot.phylo

Plot Phylogenies
trans

Translation from DNA to Amino Acid Sequences
vcv2phylo

Variance-Covariance Matrix to Tree
read.tree

Read Tree File in Parenthetic Format
weight.taxo

Define Similarity Matrix
zoom

Zoom on a Portion of a Phylogeny
reconstruct

Continuous Ancestral Character Estimation
write.nexus.data

Write Character Data in NEXUS Format
varcomp

Compute Variance Component Estimates
vcv

Phylogenetic Variance-covariance or Correlation Matrix
yule.time

Fits the Time-Dependent Yule Model
yule.cov

Fits the Yule Model With Covariates
rotate

Swapping Sister Clades
rtree

Generate Random Trees
triangMtd

Tree Reconstruction Based on the Triangles Method
unique.multiPhylo

Revomes Duplicate Trees
where

Find Patterns in DNA Sequences
which.edge

Identifies Edges of a Tree
yule

Fits the Yule Model to a Phylogenetic Tree
write.tree

Write Tree File in Parenthetic Format