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