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Install
install.packages('ape')
Monthly Downloads
55,307
Version
5.3
License
GPL (>= 2)
Maintainer
Emmanuel Paradis
Last Published
March 17th, 2019
Functions in ape (5.3)
Search functions
axisPhylo
Axis on Side of Phylogeny
dnds
dN/dS Ratio
alview
Print DNA or AA Sequence Alignement
all.equal.phylo
Global Comparison of two Phylogenies
dbd
Probability Density Under Birth--Death Models
comparePhylo
Compare Two "phylo" Objects
cophyloplot
Plots two phylogenetic trees face to face with links between the tips.
compar.ou
Ornstein--Uhlenbeck Model for Continuous Characters
corBlomberg
Blomberg et al.'s Correlation Structure
def
Definition of Vectors for Plotting or Annotating
add.scale.bar
Add a Scale Bar to a Phylogeny Plot
Moran.I
Moran's I Autocorrelation Index
alex
Alignment Explorer With Multiple Devices
ape-package
Analyses of Phylogenetics and Evolution
ape-internal
Internal Ape Functions
bd.ext
Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
base.freq
Base frequencies from DNA Sequences
branching.times
Branching Times of a Phylogenetic Tree
c.phylo
Building Lists of Trees
drop.tip
Remove Tips in a Phylogenetic Tree
balance
Balance of a Dichotomous Phylogenetic Tree
bird.families
Phylogeny of the Families of Birds From Sibley and Ahlquist
kronoviz
Plot Multiple Chronograms on the Same Scale
mantel.test
Mantel Test for Similarity of Two Matrices
is.ultrametric
Test if a Tree is Ultrametric
bird.orders
Phylogeny of the Orders of Birds From Sibley and Ahlquist
as.phylo
Conversion Among Tree and Network Objects
apetools
Tools to Explore Files
as.alignment
Conversion Among DNA Sequence Internal Formats
mat3
Three Matrices
additive
Incomplete Distance Matrix Filling
coalescent.intervals
Coalescent Intervals
all.equal.DNAbin
Compare DNA Sets
bd.time
Time-Dependent Birth-Death Models
collapse.singles
Collapse Single Nodes
as.bitsplits
Split Frequencies and Conversion Among Split Classes
compar.gee
Comparative Analysis with GEEs
phydataplot
Tree Annotation
print.phylo
Compact Display of a Phylogeny
pcoa
Principal Coordinate Analysis
as.phylo.formula
Conversion from Taxonomy Variables to Phylogenetic Trees
compar.lynch
Lynch's Comparative Method
binaryPGLMM
Phylogenetic Generalized Linear Mixed Model for Binary Data
checkAlignment
Check DNA Alignments
as.matching
Conversion Between Phylo and Matching Objects
carnivora
Carnivora body sizes and life history traits
rDNAbin
Random DNA Sequences
birthdeath
Estimation of Speciation and Extinction Rates With Birth-Death Models
read.gff
Read GFF Files
read.nexus
Read Tree File in Nexus Format
boot.phylo
Tree Bipartition and Bootstrapping Phylogenies
bind.tree
Binds Trees
checkLabel
Checking Labels
woodmouse
Cytochrome b Gene Sequences of Woodmice
chronopl
Molecular Dating With Penalized Likelihood
chronoMPL
Molecular Dating With Mean Path Lengths
checkValidPhylo
Check the Structure of a "phylo" Object
BIONJ
Tree Estimation Based on an Improved Version of the NJ Algorithm
chronos
Molecular Dating by Penalised Likelihood and Maximum Likelihood
consensus
Concensus Trees
write.dna
Write DNA Sequences in a File
cherry
Number of Cherries and Null Models of Trees
corPagel
Pagel's ``lambda'' Correlation Structure
chiroptera
Bat Phylogeny
delta.plot
Delta Plots
del.gaps
Delete Alignment Gaps in DNA Sequences
corphylo
Correlations among Multiple Traits with Phylogenetic Signal
cophenetic.phylo
Pairwise Distances from a Phylogenetic Tree
dist.dna
Pairwise Distances from DNA Sequences
corBrownian
Brownian Correlation Structure
compute.brlen
Branch Lengths Computation
howmanytrees
Calculate Numbers of Phylogenetic Trees
corClasses
Phylogenetic Correlation Structures
identify.phylo
Graphical Identification of Nodes and Tips
is.compatible
Check Compatibility of Splits
is.monophyletic
Is Group Monophyletic
makeLabel
Label Management
compute.brtime
Compute and Set Branching Times
clustal
Multiple Sequence Alignment with External Applications
makeNodeLabel
Makes Node Labels
dist.gene
Pairwise Distances from Genetic Data
gammaStat
Gamma-Statistic of Pybus and Harvey
correlogram.formula
Phylogenetic Correlogram
hivtree
Phylogenetic Tree of 193 HIV-1 Sequences
collapsed.intervals
Collapsed Coalescent Intervals
compar.cheverud
Cheverud's Comparative Method
corGrafen
Grafen's (1989) Correlation Structure
data.nex
NEXUS Data Example
label2table
Label Management
corMartins
Martins's (1997) Correlation Structure
dist.topo
Topological Distances Between Two Trees
diversi.time
Analysis of Diversification with Survival Models
diversity.contrast.test
Diversity Contrast Test
diversi.gof
Tests of Constant Diversification Rates
ladderize
Ladderize a Tree
edges
Draw Additional Edges on a Plotted Tree
image.DNAbin
Plot of DNA Sequence Alignement
evonet
Evolutionary Networks
njs
Tree Reconstruction from Incomplete Distances With NJ* or bio-NJ*
matexpo
Matrix Exponential
ewLasso
Incomplete distances and edge weights of unrooted topology
is.binary
Test for Binary Tree
mcmc.popsize
Reversible Jump MCMC to Infer Demographic History
FastME
Tree Estimation Based on the Minimum Evolution Algorithm
node.dating
node.dating
lmorigin
Multiple regression through the origin
mcconwaysims.test
McConway-Sims Test of Homogeneous Diversification
node.depth
Depth and Heights of Nodes and Tips
pic.ortho
Phylogenetically Independent Orthonormal Contrasts
plot.correlogram
Plot a Correlogram
rTraitMult
Multivariate Character Simulation
mrca
Find Most Recent Common Ancestors Between Pairs
mst
Minimum Spanning Tree
ltt.plot
Lineages Through Time Plot
read.GenBank
Read DNA Sequences from GenBank via Internet
mixedFontLabel
Mixed Font Labels for Plotting
nodelabels
Labelling the Nodes, Tips, and Edges of a Tree
nodepath
Find Paths of Nodes
phymltest
Fits a Bunch of Models with PhyML
mat5M3ID
Five Trees
pic
Phylogenetically Independent Contrasts
plot.varcomp
Plot Variance Components
parafit
Test of host-parasite coevolution
multi2di
Collapse and Resolve Multichotomies
rTraitCont
Continuous Character Simulation
reconstruct
Continuous Ancestral Character Estimation
mat5Mrand
Five Independent Trees
mvr
Minimum Variance Reduction
plotTreeTime
Plot Tree With Time Axis
read.nexus.data
Read Character Data In NEXUS Format
reorder.phylo
Internal Reordering of Trees
multiphylo
Manipulating Lists of Trees
rTraitDisc
Discrete Character Simulation
nj
Neighbor-Joining Tree Estimation
root
Roots Phylogenetic Trees
plot.phylo
Plot Phylogenies
plot.phylo.extra
Extra Fuctions to Plot and Annotate Phylogenies
read.caic
Read Tree File in CAIC Format
read.tree
Read Tree File in Parenthetic Format
speciesTree
Species Tree Estimation
subtreeplot
Zoom on a Portion of a Phylogeny by Successive Clicks
stree
Generates Systematic Regular Trees
subtrees
All subtrees of a Phylogenetic Tree
rtree
Generates Random Trees
rotate
Swapping Sister Clades
triangMtd
Tree Reconstruction Based on the Triangles Method
seg.sites
Find Segregating Sites in DNA Sequences
rtt
Root a Tree by Root-to-Tip Regression
skyline
Skyline Plot Estimate of Effective Population Size
treePop
Tree Popping
trex
Tree Explorer With Multiple Devices
read.dna
Read DNA Sequences in a File
summary.phylo
Print Summary of a Phylogeny
unique.multiPhylo
Revomes Duplicate Trees
updateLabel
Update Labels
varCompPhylip
Variance Components with Orthonormal Contrasts
write.tree
Write Tree File in Parenthetic Format
yule
Fits the Yule Model to a Phylogenetic Tree
yule.cov
Fits the Yule Model With Covariates
trans
Translation from DNA to Amino Acid Sequences
richness.yule.test
Test of Diversification-Shift With the Yule Process
yule.time
Fits the Time-Dependent Yule Model
rlineage
Tree Simulation Under the Time-Dependent Birth--Death Models
write.nexus
Write Tree File in Nexus Format
write.nexus.data
Write Character Data in NEXUS Format
vcv2phylo
Variance-Covariance Matrix to Tree
zoom
Zoom on a Portion of a Phylogeny
weight.taxo
Define Similarity Matrix
skylineplot
Drawing Skyline Plot Graphs
slowinskiguyer.test
Slowinski-Guyer Test of Homogeneous Diversification
varcomp
Compute Variance Component Estimates
vcv
Phylogenetic Variance-covariance or Correlation Matrix
where
Find Patterns in DNA Sequences
which.edge
Identifies Edges of a Tree
AAbin
Amino Acid Sequences
DNAbin2indel
Recode Blocks of Indels
Initialize.corPhyl
Initialize a `corPhyl' Structure Object
MPR
Most Parsimonious Reconstruction
DNAbin
Manipulate DNA Sequences in Bit-Level Format
SDM
Construction of Consensus Distance Matrix With SDM
LTT
Theoretical Lineage-Through Time Plots
ace
Ancestral Character Estimation
CADM.global
Congruence among distance matrices