ape v5.4-1


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Analyses of Phylogenetics and Evolution

Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.

Functions in ape

Name Description
ace Ancestral Character Estimation
CADM.global Congruence among distance matrices
DNAbin2indel Recode Blocks of Indels
DNAbin Manipulate DNA Sequences in Bit-Level Format
Initialize.corPhyl Initialize a `corPhyl' Structure Object
Moran.I Moran's I Autocorrelation Index
MPR Most Parsimonious Reconstruction
AAbin Amino Acid Sequences
LTT Theoretical Lineage-Through Time Plots
alex Alignment Explorer With Multiple Devices
bd.ext Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
SDM Construction of Consensus Distance Matrix With SDM
add.scale.bar Add a Scale Bar to a Phylogeny Plot
all.equal.DNAbin Compare DNA Sets
base.freq Base frequencies from DNA Sequences
all.equal.phylo Global Comparison of two Phylogenies
apetools Tools to Explore Files
birthdeath Estimation of Speciation and Extinction Rates With Birth-Death Models
additive Incomplete Distance Matrix Filling
boot.phylo Tree Bipartition and Bootstrapping Phylogenies
balance Balance of a Dichotomous Phylogenetic Tree
as.alignment Conversion Among DNA Sequence Internal Formats
ape-package Analyses of Phylogenetics and Evolution
ape-internal Internal Ape Functions
as.bitsplits Split Frequencies and Conversion Among Split Classes
cherry Number of Cherries and Null Models of Trees
axisPhylo Axis on Side of Phylogeny
bind.tree Binds Trees
as.matching Conversion Between Phylo and Matching Objects
BIONJ Tree Estimation Based on an Improved Version of the NJ Algorithm
branching.times Branching Times of a Phylogenetic Tree
bd.time Time-Dependent Birth-Death Models
binaryPGLMM Phylogenetic Generalized Linear Mixed Model for Binary Data
chronoMPL Molecular Dating With Mean Path Lengths
compar.ou Ornstein--Uhlenbeck Model for Continuous Characters
comparePhylo Compare Two "phylo" Objects
c.phylo Building Lists of Trees
bird.orders Phylogeny of the Orders of Birds From Sibley and Ahlquist
coalescent.intervals Coalescent Intervals
del.gaps Delete Alignment Gaps in DNA Sequences
bird.families Phylogeny of the Families of Birds From Sibley and Ahlquist
corphylo Correlations among Multiple Traits with Phylogenetic Signal
corPagel Pagel's ``lambda'' Correlation Structure
dnds dN/dS Ratio
chronopl Molecular Dating With Penalized Likelihood
corBrownian Brownian Correlation Structure
kronoviz Plot Multiple Chronograms on the Same Scale
delta.plot Delta Plots
drop.tip Remove Tips in a Phylogenetic Tree
consensus Concensus Trees
label2table Label Management
checkValidPhylo Check the Structure of a "phylo" Object
checkLabel Checking Labels
alview Print DNA or AA Sequence Alignement
compar.gee Comparative Analysis with GEEs
chiroptera Bat Phylogeny
as.phylo Conversion Among Tree and Network Objects
collapse.singles Collapse Single Nodes
compar.lynch Lynch's Comparative Method
as.phylo.formula Conversion from Taxonomy Variables to Phylogenetic Trees
mrca Find Most Recent Common Ancestors Between Pairs
makeNodeLabel Makes Node Labels
makeLabel Label Management
checkAlignment Check DNA Alignments
diversi.time Analysis of Diversification with Survival Models
chronos Molecular Dating by Penalised Likelihood and Maximum Likelihood
edges Draw Additional Edges on a Plotted Tree
cophenetic.phylo Pairwise Distances from a Phylogenetic Tree
carnivora Carnivora body sizes and life history traits
diversity.contrast.test Diversity Contrast Test
clustal Multiple Sequence Alignment with External Applications
compute.brlen Branch Lengths Computation
compute.brtime Compute and Set Branching Times
compar.cheverud Cheverud's Comparative Method
correlogram.formula Phylogenetic Correlogram
corGrafen Grafen's (1989) Correlation Structure
corMartins Martins's (1997) Correlation Structure
collapsed.intervals Collapsed Coalescent Intervals
cophyloplot Plots two phylogenetic trees face to face with links between the tips.
corBlomberg Blomberg et al.'s Correlation Structure
dist.topo Topological Distances Between Two Trees
mst Minimum Spanning Tree
latag2n Leading and Trailing Alignment Gaps to N
diversi.gof Tests of Constant Diversification Rates
ladderize Ladderize a Tree
evonet Evolutionary Networks
plot.correlogram Plot a Correlogram
pic.ortho Phylogenetically Independent Orthonormal Contrasts
multi2di Collapse and Resolve Multichotomies
is.monophyletic Is Group Monophyletic
gammaStat Gamma-Statistic of Pybus and Harvey
corClasses Phylogenetic Correlation Structures
mat5M3ID Five Trees
getAnnotationsGenBank Read Annotations from GenBank
mat5Mrand Five Independent Trees
rTraitMult Multivariate Character Simulation
data.nex NEXUS Data Example
lmorigin Multiple regression through the origin
is.ultrametric Test if a Tree is Ultrametric
dist.dna Pairwise Distances from DNA Sequences
speciesTree Species Tree Estimation
read.GenBank Read DNA Sequences from GenBank via Internet
dist.gene Pairwise Distances from Genetic Data
summary.phylo Print Summary of a Phylogeny
stree Generates Systematic Regular Trees
dbd Probability Density Under Birth--Death Models
nodepath Find Paths of Nodes
njs Tree Reconstruction from Incomplete Distances With NJ* or bio-NJ*
ltt.plot Lineages Through Time Plot
hivtree Phylogenetic Tree of 193 HIV-1 Sequences
parafit Test of host-parasite coevolution
trans Translation from DNA to Amino Acid Sequences
def Definition of Vectors for Plotting or Annotating
write.nexus.data Write Character Data in NEXUS Format
multiphylo Manipulating Lists of Trees
write.nexus Write Tree File in Nexus Format
write.tree Write Tree File in Parenthetic Format
yule Fits the Yule Model to a Phylogenetic Tree
howmanytrees Calculate Numbers of Phylogenetic Trees
ewLasso Incomplete distances and edge weights of unrooted topology
FastME Tree Estimation Based on the Minimum Evolution Algorithm
is.binary Test for Binary Tree
is.compatible Check Compatibility of Splits
node.depth Depth and Heights of Nodes and Tips
nodelabels Labelling the Nodes, Tips, and Edges of a Tree
identify.phylo Graphical Identification of Nodes and Tips
node.dating node.dating
print.phylo Compact Display of a Phylogeny
read.gff Read GFF Files
seg.sites Find Segregating Sites in DNA Sequences
skyline Skyline Plot Estimate of Effective Population Size
read.nexus Read Tree File in Nexus Format
rDNAbin Random DNA Sequences
mvr Minimum Variance Reduction
mat3 Three Matrices
image.DNAbin Plot of DNA Sequence Alignement
mantel.test Mantel Test for Similarity of Two Matrices
mcconwaysims.test McConway-Sims Test of Homogeneous Diversification
richness.yule.test Test of Diversification-Shift With the Yule Process
matexpo Matrix Exponential
rTraitCont Continuous Character Simulation
rlineage Tree Simulation Under the Time-Dependent Birth--Death Models
root Roots Phylogenetic Trees
nj Neighbor-Joining Tree Estimation
phydataplot Tree Annotation
pcoa Principal Coordinate Analysis
plot.phylo Plot Phylogenies
mixedFontLabel Mixed Font Labels for Plotting
mcmc.popsize Reversible Jump MCMC to Infer Demographic History
phymltest Fits a Bunch of Models with PhyML
plot.phylo.extra Extra Fuctions to Plot and Annotate Phylogenies
read.nexus.data Read Character Data In NEXUS Format
pic Phylogenetically Independent Contrasts
trex Tree Explorer With Multiple Devices
rTraitDisc Discrete Character Simulation
treePop Tree Popping
where Find Patterns in DNA Sequences
updateLabel Update Labels
plot.varcomp Plot Variance Components
rotate Swapping Sister Clades
plotTreeTime Plot Tree With Time Axis
read.tree Read Tree File in Parenthetic Format
which.edge Identifies Edges of a Tree
varCompPhylip Variance Components with Orthonormal Contrasts
read.caic Read Tree File in CAIC Format
reconstruct Continuous Ancestral Character Estimation
rtree Generates Random Trees
rtt Root a Tree by Root-to-Tip Regression
subtrees All subtrees of a Phylogenetic Tree
zoom Zoom on a Portion of a Phylogeny
reorder.phylo Internal Reordering of Trees
read.dna Read DNA Sequences in a File
slowinskiguyer.test Slowinski-Guyer Test of Homogeneous Diversification
vcv Phylogenetic Variance-covariance or Correlation Matrix
varcomp Compute Variance Component Estimates
skylineplot Drawing Skyline Plot Graphs
triangMtd Tree Reconstruction Based on the Triangles Method
subtreeplot Zoom on a Portion of a Phylogeny by Successive Clicks
vcv2phylo Variance-Covariance Matrix to Tree
weight.taxo Define Similarity Matrix
woodmouse Cytochrome b Gene Sequences of Woodmice
unique.multiPhylo Revomes Duplicate Trees
write.dna Write DNA Sequences in a File
yule.time Fits the Time-Dependent Yule Model
yule.cov Fits the Yule Model With Covariates
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