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Install
install.packages('ape')
Monthly Downloads
71,581
Version
5.1
License
GPL (>= 2)
Maintainer
Emmanuel Paradis
Last Published
April 4th, 2018
Functions in ape (5.1)
Search functions
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