ape v3.1-3

0

Monthly downloads

0th

Percentile

Analyses of Phylogenetics and Evolution

ape provides 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 allelic and nucleotide data, reading and writing nucleotide sequences, 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. 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
compar.cheverud Cheverud's Comparative Method
chiroptera Bat Phylogeny
compute.brlen Branch Lengths Computation
del.gaps Delete Alignment Gaps in DNA Sequences
diversity.contrast.test Diversity Contrast Test
compar.gee Comparative Analysis with GEEs
read.GenBank Read DNA Sequences from GenBank via Internet
mat3 Three Matrices
read.tree Read Tree File in Parenthetic Format
branching.times Branching Times of a Phylogenetic Tree
reorder.phylo Internal Reordering of Trees
nj Neighbor-Joining Tree Estimation
multi2di Collapse and Resolve Multichotomies
ltt.plot Lineages Through Time Plot
matexpo Matrix Exponential
write.nexus Write Tree File in Nexus Format
mat5Mrand Five Independent Trees
kronoviz Plot Multiple Chronograms on the Same Scale
is.monophyletic Is Group Monophyletic
is.compatible Check Compatibility of Splits
DNAbin Manipulate DNA Sequences in Bit-Level Format
write.tree Write Tree File in Parenthetic Format
data.nex NEXUS Data Example
compar.lynch Lynch's Comparative Method
collapsed.intervals Collapsed Coalescent Intervals
image.DNAbin Plot of DNA Sequence Alignement
opsin Gene Tree of 32 opsin Sequences
as.matching Conversion Between Phylo and Matching Objects
is.ultrametric Test if a Tree is Ultrametric
bd.ext Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
treePop Tree Popping
mat5M3ID Five Trees
carnivora Carnivora body sizes and life history traits
speciesTree Species Tree Estimation
bd.time Time-Dependent Birth-Death Models
rTraitCont Continuous Character Simulation
bind.tree Binds Trees
corMartins Martins's (1997) Correlation Structure
skylineplot Drawing Skyline Plot Graphs
edges Draw Additional Edges on a Plotted Tree
corPagel Pagel's ``lambda'' Correlation Structure
mvr Minimum Variance Reduction
chronoMPL Molecular Dating With Mean Path Lengths
corBrownian Brownian Correlation Structure
dist.gene Pairwise Distances from Genetic Data
as.bitsplits Split Frequencies and Conversion Among Split Classes
pic.ortho Phylogenetically Independent Orthonormal Contrasts
rTraitMult Multivariate Character Simulation
Moran.I Moran's I Autocorrelation Index
diversi.gof Tests of Constant Diversification Rates
LTT Theoretical Lineage-Through Time Plots
cophenetic.phylo Pairwise Distances from a Phylogenetic Tree
FastME Tree Estimation Based on the Minimum Evolution Algorithm
coalescent.intervals Coalescent Intervals
pic Phylogenetically Independent Contrasts
read.dna Read DNA Sequences in a File
yule.cov Fits the Yule Model With Covariates
pcoa Principal Coordinate Analysis
collapse.singles Collapse Single Nodes
phydataplot Tree Annotation
write.dna Write DNA Sequences in a File
mcconwaysims.test McConway-Sims Test of Homogeneous Diversification
cherry Number of Cherries and Null Models of Trees
ace Ancestral Character Estimation
mst Minimum Spanning Tree
chronopl Molecular Dating With Penalized Likelihood
makeLabel Label Management
yule Fits the Yule Model to a Phylogenetic Tree
consensus Concensus Trees
phymltest Fits a Bunch of Models with PhyML
dist.dna Pairwise Distances from DNA Sequences
read.nexus Read Tree File in Nexus Format
mantel.test Mantel Test for Similarity of Two Matrices
SDM Construction of Consensus Distance Matrix With SDM
compute.brtime Compute and Set Branching Times
hivtree Phylogenetic Tree of 193 HIV-1 Sequences
ape-internal Internal Ape Functions
c.phylo Building Lists of Trees
ape-package Analyses of Phylogenetics and Evolution
mrca Find Most Recent Common Ancestors Between Pairs
compar.ou Ornstein--Uhlenbeck Model for Continuous Characters
evonet Evolutionary Networks
makeNodeLabel Makes Node Labels
cophyloplot Plots two phylogenetic trees face to face with links between the tips.
ladderize Ladderize a Tree
clustal Multiple Sequence Alignment with External Applications
corGrafen Grafen's (1989) Correlation Structure
unique.multiPhylo Revomes Duplicate Trees
subtrees All subtrees of a Phylogenetic Tree
njs Tree Reconstruction from Incomplete Distances With NJ* or bio-NJ*
which.edge Identifies Edges of a Tree
slowinskiguyer.test Slowinski-Guyer Test of Homogeneous Diversification
where Find Patterns in DNA Sequences
triangMtd Tree Reconstruction Based on the Triangles Method
woodmouse Cytochrome b Gene Sequences of Woodmice
seg.sites Find Segregating Sites in DNA Sequences
weight.taxo Define Similarity Matrix
subtreeplot Zoom on a Portion of a Phylogeny by Successive Clicks
bird.orders Phylogeny of the Orders of Birds From Sibley and Ahlquist
rotate Swapping Sister Clades
varcomp Compute Variance Component Estimates
summary.phylo Print Summary of a Phylogeny
rtt Root a Tree by Root-to-Tip Regression
trex Tree Explorer With Multiple Devices
rtree Generates Random Trees
richness.yule.test Test of Diversification-Shift With the Yule Process
plot.varcomp Plot Variance Components
root Roots Phylogenetic Trees
axisPhylo Axis on Side of Phylogeny
skyline Skyline Plot Estimate of Effective Population Size
parafit Test of host-parasite coevolution
multiphylo Manipulating Lists of Trees
delta.plot Delta Plots
as.alignment Conversion Among DNA Sequence Internal Formats
varCompPhylip Variance Components with Orthonormal Contrasts
dbd Probability Density Under Birth--Death Models
stree Generates Systematic Regular Trees
all.equal.phylo Global Comparison of two Phylogenies
rTraitDisc Discrete Character Simulation
vcv Phylogenetic Variance-covariance or Correlation Matrix
base.freq Base frequencies from DNA Sequences
as.phylo.formula Conversion from Taxonomy Variables to Phylogenetic Trees
add.scale.bar Add a Scale Bar to a Phylogeny Plot
read.nexus.data Read Character Data In NEXUS Format
print.phylo Compact Display of a Phylogeny
plot.correlogram Plot a Correlogram
corClasses Phylogenetic Correlation Structures
node.depth Depth and Heights of Nodes and Tips
Initialize.corPhyl Initialize a `corPhyl' Structure Object
mcmc.popsize Reversible Jump MCMC to Infer Demographic History
alex Alignment Explorer With Multiple Devices
birthdeath Estimation of Speciation and Extinction Rates With Birth-Death Models
lmorigin Multiple regression through the origin
yule.time Fits the Time-Dependent Yule Model
boot.phylo Tree Bipartition and Bootstrapping Phylogenies
zoom Zoom on a Portion of a Phylogeny
plot.phylo Plot Phylogenies
landplants Gene Tree of 36 Landplant rbcL Sequences
is.binary.tree Test for Binary Tree
corBlomberg Blomberg et al.'s Correlation Structure
nodelabels Labelling the Nodes, Tips, and Edges of a Tree
mixedFontLabel Mixed Font Labels for Plotting
write.nexus.data Write Character Data in NEXUS Format
CADM.global Congruence among distance matrices
as.phylo Conversion Among Tree and Network Objects
read.caic Read Tree File in CAIC Format
diversi.time Analysis of Diversification with Survival Models
chronos Molecular Dating by Penalised Likelihood and Maximum Likelihood
rlineage Tree Simulation Under the Time-Dependent Birth--Death Models
howmanytrees Calculate Numbers of Phylogenetic Trees
dist.topo Topological Distances Between Two Trees
ewLasso Incomplete distances and edge weights of unrooted topology
identify.phylo Graphical Identification of Nodes and Tips
drop.tip Remove Tips in a Phylogenetic Tree
balance Balance of a Dichotomous Phylogenetic Tree
additive Incomplete Distance Matrix Filling
MPR Most Parsimonious Reconstruction
correlogram.formula Phylogenetic Correlogram
bird.families Phylogeny of the Families of Birds From Sibley and Ahlquist
BIONJ Tree Estimation Based on an Improved Version of the NJ Algorithm
gammaStat Gamma-Statistic of Pybus and Harvey
No Results!

Last month downloads

Details

Include our badge in your README

[![Rdoc](http://www.rdocumentation.org/badges/version/ape)](http://www.rdocumentation.org/packages/ape)