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Install
install.packages('ape')
Monthly Downloads
72,088
Version
5.0
License
GPL (>= 2)
Maintainer
Emmanuel Paradis
Last Published
October 30th, 2017
Functions in ape (5.0)
Search functions
SDM
Construction of Consensus Distance Matrix With SDM
ace
Ancestral Character Estimation
apetools
Tools to Explore Files
as.alignment
Conversion Among DNA Sequence Internal Formats
as.phylo
Conversion Among Tree and Network Objects
as.phylo.formula
Conversion from Taxonomy Variables to Phylogenetic Trees
carnivora
Carnivora body sizes and life history traits
checkAlignment
Check DNA Alignments
collapse.singles
Collapse Single Nodes
collapsed.intervals
Collapsed Coalescent Intervals
compar.lynch
Lynch's Comparative Method
compar.ou
Ornstein--Uhlenbeck Model for Continuous Characters
corPagel
Pagel's ``lambda'' Correlation Structure
corphylo
Correlations among Multiple Traits with Phylogenetic Signal
dist.dna
Pairwise Distances from DNA Sequences
dist.gene
Pairwise Distances from Genetic Data
identify.phylo
Graphical Identification of Nodes and Tips
DNAbin
Manipulate DNA Sequences in Bit-Level Format
DNAbin2indel
Recode Blocks of Indels
add.scale.bar
Add a Scale Bar to a Phylogeny Plot
additive
Incomplete Distance Matrix Filling
axisPhylo
Axis on Side of Phylogeny
image.DNAbin
Plot of DNA Sequence Alignement
ladderize
Ladderize a Tree
lmorigin
Multiple regression through the origin
mcconwaysims.test
McConway-Sims Test of Homogeneous Diversification
mcmc.popsize
Reversible Jump MCMC to Infer Demographic History
nj
Neighbor-Joining Tree Estimation
njs
Tree Reconstruction from Incomplete Distances With NJ* or bio-NJ*
plotTreeTime
Plot Tree With Time Axis
print.phylo
Compact Display of a Phylogeny
rTraitMult
Multivariate Character Simulation
balance
Balance of a Dichotomous Phylogenetic Tree
bind.tree
Binds Trees
BIONJ
Tree Estimation Based on an Improved Version of the NJ Algorithm
chronopl
Molecular Dating With Penalized Likelihood
chronos
Molecular Dating by Penalised Likelihood and Maximum Likelihood
compar.cheverud
Cheverud's Comparative Method
compar.gee
Comparative Analysis with GEEs
corGrafen
Grafen's (1989) Correlation Structure
corMartins
Martins's (1997) Correlation Structure
drop.tip
Remove Tips in a Phylogenetic Tree
edges
Draw Additional Edges on a Plotted Tree
read.GenBank
Read DNA Sequences from GenBank via Internet
rtree
Generates Random Trees
rtt
Root a Tree by Root-to-Tip Regression
speciesTree
Species Tree Estimation
hivtree
Phylogenetic Tree of 193 HIV-1 Sequences
howmanytrees
Calculate Numbers of Phylogenetic Trees
kronoviz
Plot Multiple Chronograms on the Same Scale
label2table
Label Management
mixedFontLabel
Mixed Font Labels for Plotting
vcv
Phylogenetic Variance-covariance or Correlation Matrix
vcv2phylo
Variance-Covariance Matrix to Tree
stree
Generates Systematic Regular Trees
write.dna
Write DNA Sequences in a File
write.nexus
Write Tree File in Nexus Format
mrca
Find Most Recent Common Ancestors Between Pairs
multiphylo
Manipulating Lists of Trees
mvr
Minimum Variance Reduction
plot.correlogram
Plot a Correlogram
plot.phylo
Plot Phylogenies
rTraitCont
Continuous Character Simulation
rTraitDisc
Discrete Character Simulation
reconstruct
Continuous Ancestral Character Estimation
reorder.phylo
Internal Reordering of Trees
treePop
Tree Popping
trex
Tree Explorer With Multiple Devices
varCompPhylip
Variance Components with Orthonormal Contrasts
varcomp
Compute Variance Component Estimates
yule
Fits the Yule Model to a Phylogenetic Tree
yule.cov
Fits the Yule Model With Covariates
all.equal.DNAbin
Compare DNA Sets
bd.time
Time-Dependent Birth-Death Models
binaryPGLMM
Phylogenetic Generalized Linear Mixed Model for Binary Data
seg.sites
Find Segregating Sites in DNA Sequences
skyline
Skyline Plot Estimate of Effective Population Size
subtreeplot
Zoom on a Portion of a Phylogeny by Successive Clicks
subtrees
All subtrees of a Phylogenetic Tree
which.edge
Identifies Edges of a Tree
woodmouse
Cytochrome b Gene Sequences of Woodmice
yule.time
Fits the Time-Dependent Yule Model
zoom
Zoom on a Portion of a Phylogeny
multi2di
Collapse and Resolve Multichotomies
MPR
Most Parsimonious Reconstruction
Moran.I
Moran's I Autocorrelation Index
alex
Alignment Explorer With Multiple Devices
AAbin
Amino Acid Sequences
CADM.global
Congruence among distance matrices
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
branching.times
Branching Times of a Phylogenetic Tree
c.phylo
Building Lists of Trees
chiroptera
Bat Phylogeny
base.freq
Base frequencies from DNA Sequences
chronoMPL
Molecular Dating With Mean Path Lengths
consensus
Concensus Trees
cophenetic.phylo
Pairwise Distances from a Phylogenetic Tree
correlogram.formula
Phylogenetic Correlogram
data.nex
NEXUS Data Example
dist.topo
Topological Distances Between Two Trees
diversi.gof
Tests of Constant Diversification Rates
FastME
Tree Estimation Based on the Minimum Evolution Algorithm
gammaStat
Gamma-Statistic of Pybus and Harvey
bird.families
Phylogeny of the Families of Birds From Sibley and Ahlquist
bird.orders
Phylogeny of the Orders of Birds From Sibley and Ahlquist
all.equal.phylo
Global Comparison of two Phylogenies
alview
Print DNA or AA Sequence Alignement
ltt.plot
Lineages Through Time Plot
makeLabel
Label Management
mat5Mrand
Five Independent Trees
matexpo
Matrix Exponential
parafit
Test of host-parasite coevolution
pcoa
Principal Coordinate Analysis
pic
Phylogenetically Independent Contrasts
pic.ortho
Phylogenetically Independent Orthonormal Contrasts
read.caic
Read Tree File in CAIC Format
read.dna
Read DNA Sequences in a File
richness.yule.test
Test of Diversification-Shift With the Yule Process
rlineage
Tree Simulation Under the Time-Dependent Birth--Death Models
skylineplot
Drawing Skyline Plot Graphs
slowinskiguyer.test
Slowinski-Guyer Test of Homogeneous Diversification
dbd
Probability Density Under Birth--Death Models
compute.brlen
Branch Lengths Computation
compute.brtime
Compute and Set Branching Times
corBrownian
Brownian Correlation Structure
corClasses
Phylogenetic Correlation Structures
weight.taxo
Define Similarity Matrix
where
Find Patterns in DNA Sequences
write.nexus.data
Write Character Data in NEXUS Format
write.tree
Write Tree File in Parenthetic Format
def
Definition of Vectors for Plotting or Annotating
is.ultrametric
Test if a Tree is Ultrametric
mst
Minimum Spanning Tree
nodelabels
Labelling the Nodes, Tips, and Edges of a Tree
nodepath
Find Paths of Nodes
phydataplot
Tree Annotation
phymltest
Fits a Bunch of Models with PhyML
is.monophyletic
Is Group Monophyletic
read.gff
Read GFF Files
read.nexus
Read Tree File in Nexus Format
root
Roots Phylogenetic Trees
rotate
Swapping Sister Clades
mat3
Three Matrices
mat5M3ID
Five Trees
summary.phylo
Print Summary of a Phylogeny
trans
Translation from DNA to Amino Acid Sequences
triangMtd
Tree Reconstruction Based on the Triangles Method
unique.multiPhylo
Revomes Duplicate Trees
Initialize.corPhyl
Initialize a `corPhyl' Structure Object
LTT
Theoretical Lineage-Through Time Plots
as.bitsplits
Split Frequencies and Conversion Among Split Classes
checkValidPhylo
Check the Structure of a "phylo" Object
cherry
Number of Cherries and Null Models of Trees
diversi.time
Analysis of Diversification with Survival Models
diversity.contrast.test
Diversity Contrast Test
as.matching
Conversion Between Phylo and Matching Objects
is.binary
Test for Binary Tree
is.compatible
Check Compatibility of Splits
cophyloplot
Plots two phylogenetic trees face to face with links between the tips.
corBlomberg
Blomberg et al.'s Correlation Structure
del.gaps
Delete Alignment Gaps in DNA Sequences
delta.plot
Delta Plots
makeNodeLabel
Makes Node Labels
mantel.test
Mantel Test for Similarity of Two Matrices
read.nexus.data
Read Character Data In NEXUS Format
read.tree
Read Tree File in Parenthetic Format
clustal
Multiple Sequence Alignment with External Applications
coalescent.intervals
Coalescent Intervals
node.dating
node.dating
node.depth
Depth and Heights of Nodes and Tips
birthdeath
Estimation of Speciation and Extinction Rates With Birth-Death Models
boot.phylo
Tree Bipartition and Bootstrapping Phylogenies
evonet
Evolutionary Networks
ewLasso
Incomplete distances and edge weights of unrooted topology
plot.phylo.extra
Extra Fuctions to Plot and Annotate Phylogenies
plot.varcomp
Plot Variance Components