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Install
install.packages('ape')
Monthly Downloads
50,451
Version
5.2
License
GPL (>= 2)
Maintainer
Emmanuel Paradis
Last Published
September 24th, 2018
Functions in ape (5.2)
Search functions
ace
Ancestral Character Estimation
add.scale.bar
Add a Scale Bar to a Phylogeny Plot
as.matching
Conversion Between Phylo and Matching Objects
bird.families
Phylogeny of the Families of Birds From Sibley and Ahlquist
as.bitsplits
Split Frequencies and Conversion Among Split Classes
additive
Incomplete Distance Matrix Filling
bird.orders
Phylogeny of the Orders of Birds From Sibley and Ahlquist
collapsed.intervals
Collapsed Coalescent Intervals
comparePhylo
Compare Two "phylo" Objects
collapse.singles
Collapse Single Nodes
all.equal.phylo
Global Comparison of two Phylogenies
alview
Print DNA or AA Sequence Alignement
axisPhylo
Axis on Side of Phylogeny
as.alignment
Conversion Among DNA Sequence Internal Formats
as.phylo.formula
Conversion from Taxonomy Variables to Phylogenetic Trees
apetools
Tools to Explore Files
clustal
Multiple Sequence Alignment with External Applications
as.phylo
Conversion Among Tree and Network Objects
compute.brlen
Branch Lengths Computation
coalescent.intervals
Coalescent Intervals
cophenetic.phylo
Pairwise Distances from a Phylogenetic Tree
balance
Balance of a Dichotomous Phylogenetic Tree
base.freq
Base frequencies from DNA Sequences
carnivora
Carnivora body sizes and life history traits
bd.ext
Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
chiroptera
Bat Phylogeny
birthdeath
Estimation of Speciation and Extinction Rates With Birth-Death Models
boot.phylo
Tree Bipartition and Bootstrapping Phylogenies
corMartins
Martins's (1997) Correlation Structure
alex
Alignment Explorer With Multiple Devices
corPagel
Pagel's ``lambda'' Correlation Structure
ape-internal
Internal Ape Functions
ape-package
Analyses of Phylogenetics and Evolution
cophyloplot
Plots two phylogenetic trees face to face with links between the tips.
bd.time
Time-Dependent Birth-Death Models
all.equal.DNAbin
Compare DNA Sets
data.nex
NEXUS Data Example
bind.tree
Binds Trees
dbd
Probability Density Under Birth--Death Models
binaryPGLMM
Phylogenetic Generalized Linear Mixed Model for Binary Data
chronoMPL
Molecular Dating With Mean Path Lengths
BIONJ
Tree Estimation Based on an Improved Version of the NJ Algorithm
checkValidPhylo
Check the Structure of a "phylo" Object
cherry
Number of Cherries and Null Models of Trees
diversity.contrast.test
Diversity Contrast Test
branching.times
Branching Times of a Phylogenetic Tree
delta.plot
Delta Plots
compute.brtime
Compute and Set Branching Times
checkAlignment
Check DNA Alignments
compar.lynch
Lynch's Comparative Method
c.phylo
Building Lists of Trees
compar.gee
Comparative Analysis with GEEs
compar.cheverud
Cheverud's Comparative Method
consensus
Concensus Trees
corBlomberg
Blomberg et al.'s Correlation Structure
corClasses
Phylogenetic Correlation Structures
corGrafen
Grafen's (1989) Correlation Structure
dist.dna
Pairwise Distances from DNA Sequences
chronopl
Molecular Dating With Penalized Likelihood
drop.tip
Remove Tips in a Phylogenetic Tree
image.DNAbin
Plot of DNA Sequence Alignement
compar.ou
Ornstein--Uhlenbeck Model for Continuous Characters
corBrownian
Brownian Correlation Structure
corphylo
Correlations among Multiple Traits with Phylogenetic Signal
diversi.gof
Tests of Constant Diversification Rates
diversi.time
Analysis of Diversification with Survival Models
gammaStat
Gamma-Statistic of Pybus and Harvey
chronos
Molecular Dating by Penalised Likelihood and Maximum Likelihood
is.binary
Test for Binary Tree
edges
Draw Additional Edges on a Plotted Tree
hivtree
Phylogenetic Tree of 193 HIV-1 Sequences
howmanytrees
Calculate Numbers of Phylogenetic Trees
correlogram.formula
Phylogenetic Correlogram
label2table
Label Management
identify.phylo
Graphical Identification of Nodes and Tips
makeLabel
Label Management
makeNodeLabel
Makes Node Labels
mrca
Find Most Recent Common Ancestors Between Pairs
evonet
Evolutionary Networks
ladderize
Ladderize a Tree
matexpo
Matrix Exponential
mcconwaysims.test
McConway-Sims Test of Homogeneous Diversification
is.compatible
Check Compatibility of Splits
multi2di
Collapse and Resolve Multichotomies
dist.gene
Pairwise Distances from Genetic Data
mst
Minimum Spanning Tree
is.monophyletic
Is Group Monophyletic
def
Definition of Vectors for Plotting or Annotating
multiphylo
Manipulating Lists of Trees
del.gaps
Delete Alignment Gaps in DNA Sequences
njs
Tree Reconstruction from Incomplete Distances With NJ* or bio-NJ*
dist.topo
Topological Distances Between Two Trees
FastME
Tree Estimation Based on the Minimum Evolution Algorithm
pcoa
Principal Coordinate Analysis
ewLasso
Incomplete distances and edge weights of unrooted topology
pic.ortho
Phylogenetically Independent Orthonormal Contrasts
lmorigin
Multiple regression through the origin
plot.correlogram
Plot a Correlogram
mantel.test
Mantel Test for Similarity of Two Matrices
is.ultrametric
Test if a Tree is Ultrametric
rTraitCont
Continuous Character Simulation
kronoviz
Plot Multiple Chronograms on the Same Scale
mat3
Three Matrices
rTraitDisc
Discrete Character Simulation
ltt.plot
Lineages Through Time Plot
mvr
Minimum Variance Reduction
mixedFontLabel
Mixed Font Labels for Plotting
mcmc.popsize
Reversible Jump MCMC to Infer Demographic History
node.dating
node.dating
nj
Neighbor-Joining Tree Estimation
phymltest
Fits a Bunch of Models with PhyML
richness.yule.test
Test of Diversification-Shift With the Yule Process
phydataplot
Tree Annotation
pic
Phylogenetically Independent Contrasts
reconstruct
Continuous Ancestral Character Estimation
print.phylo
Compact Display of a Phylogeny
node.depth
Depth and Heights of Nodes and Tips
mat5M3ID
Five Trees
rlineage
Tree Simulation Under the Time-Dependent Birth--Death Models
rDNAbin
Random DNA Sequences
varcomp
Compute Variance Component Estimates
speciesTree
Species Tree Estimation
vcv
Phylogenetic Variance-covariance or Correlation Matrix
mat5Mrand
Five Independent Trees
nodepath
Find Paths of Nodes
nodelabels
Labelling the Nodes, Tips, and Edges of a Tree
yule.cov
Fits the Yule Model With Covariates
stree
Generates Systematic Regular Trees
reorder.phylo
Internal Reordering of Trees
vcv2phylo
Variance-Covariance Matrix to Tree
weight.taxo
Define Similarity Matrix
yule.time
Fits the Time-Dependent Yule Model
parafit
Test of host-parasite coevolution
rTraitMult
Multivariate Character Simulation
read.GenBank
Read DNA Sequences from GenBank via Internet
summary.phylo
Print Summary of a Phylogeny
trans
Translation from DNA to Amino Acid Sequences
where
Find Patterns in DNA Sequences
plot.phylo
Plot Phylogenies
updateLabel
Update Labels
plot.phylo.extra
Extra Fuctions to Plot and Annotate Phylogenies
which.edge
Identifies Edges of a Tree
varCompPhylip
Variance Components with Orthonormal Contrasts
zoom
Zoom on a Portion of a Phylogeny
read.nexus.data
Read Character Data In NEXUS Format
read.gff
Read GFF Files
read.nexus
Read Tree File in Nexus Format
read.tree
Read Tree File in Parenthetic Format
plot.varcomp
Plot Variance Components
plotTreeTime
Plot Tree With Time Axis
read.caic
Read Tree File in CAIC Format
skylineplot
Drawing Skyline Plot Graphs
slowinskiguyer.test
Slowinski-Guyer Test of Homogeneous Diversification
root
Roots Phylogenetic Trees
rotate
Swapping Sister Clades
woodmouse
Cytochrome b Gene Sequences of Woodmice
seg.sites
Find Segregating Sites in DNA Sequences
skyline
Skyline Plot Estimate of Effective Population Size
write.dna
Write DNA Sequences in a File
read.dna
Read DNA Sequences in a File
rtree
Generates Random Trees
triangMtd
Tree Reconstruction Based on the Triangles Method
rtt
Root a Tree by Root-to-Tip Regression
unique.multiPhylo
Revomes Duplicate Trees
subtreeplot
Zoom on a Portion of a Phylogeny by Successive Clicks
write.nexus
Write Tree File in Nexus Format
subtrees
All subtrees of a Phylogenetic Tree
treePop
Tree Popping
trex
Tree Explorer With Multiple Devices
write.tree
Write Tree File in Parenthetic Format
yule
Fits the Yule Model to a Phylogenetic Tree
write.nexus.data
Write Character Data in NEXUS Format
Initialize.corPhyl
Initialize a `corPhyl' Structure Object
LTT
Theoretical Lineage-Through Time Plots
DNAbin
Manipulate DNA Sequences in Bit-Level Format
DNAbin2indel
Recode Blocks of Indels
MPR
Most Parsimonious Reconstruction
Moran.I
Moran's I Autocorrelation Index
AAbin
Amino Acid Sequences
CADM.global
Congruence among distance matrices
SDM
Construction of Consensus Distance Matrix With SDM