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ape (version 3.0-2)

Analyses of Phylogenetics and Evolution

Description

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, minimum spanning tree, 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.

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Version

Install

install.packages('ape')

Monthly Downloads

84,031

Version

3.0-2

License

GPL (>= 2)

Maintainer

Emmanuel Paradis

Last Published

April 5th, 2012

Functions in ape (3.0-2)

cherry

Number of Cherries and Null Models of Trees
as.phylo

Conversion Among Tree and Network Objects
diversi.time

Analysis of Diversification with Survival Models
landplants

Gene Tree of 36 Landplant rbcL Sequences
MPR

Most Parsimonious Reconstruction
Moran.I

Moran's I Autocorrelation Index
SDM

Construction of Consensus Distance Matrix With SDM
add.scale.bar

Add a Scale Bar to a Phylogeny Plot
additive

Incomplete Distance Matrix Filling
balance

Balance of a Dichotomous Phylogenetic Tree
corGrafen

Grafen's (1989) Correlation Structure
collapse.singles

Collapse Single Nodes
compar.cheverud

Cheverud's Comparative Method
branching.times

Branching Times of a Phylogenetic Tree
ape-internal

Internal Ape Functions
carnivora

Carnivora body sizes and life history traits
base.freq

Base frequencies from DNA Sequences
dist.topo

Topological Distances Between Two Trees
birthdeath

Estimation of Speciation and Extinction Rates With Birth-Death Models
corBlomberg

Blomberg et al.'s Correlation Structure
as.alignment

Conversion Among DNA Sequence Internal Formats
ape-package

Analyses of Phylogenetics and Evolution
diversi.gof

Tests of Constant Diversification Rates
all.equal.phylo

Global Comparison of two Phylogenies
consensus

Concensus Trees
GC.content

Content in GC from DNA Sequences
as.bitsplits

Conversion Among Split Classes
gammaStat

Gamma-Statistic of Pybus and Harvey
correlogram.formula

Phylogenetic Correlogram
boot.phylo

Tree Bipartition and Bootstrapping Phylogenies
DNAbin

Manipulate DNA Sequences in Bit-Level Format
compar.gee

Comparative Analysis with GEEs
pic.ortho

Phylogenetically Independent Orthonormal Contrasts
collapsed.intervals

Collapsed Coalescent Intervals
stree

Generates Systematic Regular Trees
plot.varcomp

Plot Variance Components
corClasses

Phylogenetic Correlation Structures
mat5M3ID

Five Trees
image.DNAbin

Plot of DNA Sequence Alignement
rTraitCont

Continuous Character Simulation
write.dna

Write DNA Sequences in a File
seg.sites

Find Segregating Sites in DNA Sequences
read.nexus.data

Read Character Data In NEXUS Format
read.GenBank

Read DNA Sequences from GenBank via Internet
clustal

Multiple Sequence Alignment with External Applications
woodmouse

Cytochrome b Gene Sequences of Woodmice
nj

Neighbor-Joining Tree Estimation
varcomp

Compute Variance Component Estimates
read.nexus

Read Tree File in Nexus Format
as.phylo.formula

Conversion from Taxonomy Variables to Phylogenetic Trees
treePop

Tree Popping
write.nexus

Write Tree File in Nexus Format
del.gaps

Delete Alignment Gaps in DNA Sequences
is.binary.tree

Test for Binary Tree
data.nex

NEXUS Data Example
makeNodeLabel

Makes Node Labels
is.ultrametric

Test if a Tree is Ultrametric
node.depth

Depth of Nodes and Tips
is.monophyletic

Is Group Monophyletic
plot.correlogram

Plot a Correlogram
coalescent.intervals

Coalescent Intervals
bird.families

Phylogeny of the Families of Birds From Sibley and Ahlquist
mrca

Find Most Recent Common Ancestors Between Pairs
as.matching

Conversion Between Phylo and Matching Objects
ape-defunct

Defunct Ape Functions
ladderize

Ladderize a Tree
BIONJ

Tree Estimation Based on an Improved Version of the NJ Algorithm
alex

Alignment Explorer With Multiple Devices
reorder.phylo

Internal Reordering of Trees
multi2di

Collapse and Resolve Multichotomies
which.edge

Identifies Edges of a Tree
weight.taxo

Define Similarity Matrix
speciesTree

Species Tree Estimation
mantel.test

Mantel Test for Similarity of Two Matrices
write.nexus.data

Write Character Data In NEXUS Format
slowinskiguyer.test

Slowinski-Guyer Test of Homogeneous Diversification
kronoviz

Plot Multiple Chronograms on the Same Scale
read.dna

Read DNA Sequences in a File
yule.time

Fits the Time-Dependent Yule Model
multiphylo

Manipulating Lists of Trees
unique.multiPhylo

Revomes Duplicate Trees
njs

Tree Reconstruction from Incomplete Distances With NJ* or bio-NJ*
rtree

Generates Random Trees
skylineplot

Drawing Skyline Plot Graphs
read.caic

Read Tree File in CAIC Format
hivtree

Phylogenetic Tree of 193 HIV-1 Sequences
vcv

Phylogenetic Variance-covariance or Correlation Matrix
mixedFontLabel

Mixed Font Labels for Plotting
CADM.global

Congruence among distance matrices
summary.phylo

Print Summary of a Phylogeny
dist.gene

Pairwise Distances from Genetic Data
print.phylo

Compact Display of a Phylogeny
varCompPhylip

Variance Components with Orthonormal Contrasts
chronoMPL

Molecular Dating With Mean Path Lengths
opsin

Gene Tree of 32 opsin Sequences
bd.ext

Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
chronopl

Molecular Dating With Penalized Likelihood
Initialize.corPhyl

Initialize a `corPhyl' Structure Object
cophyloplot

Plots two phylogenetic trees face to face with links between the tips.
makeLabel

Label Management
matexpo

Matrix Exponential
subtrees

All subtrees of a Phylogenetic Tree
axisPhylo

Axis on Side of Phylogeny
cophenetic.phylo

Pairwise Distances from a Phylogenetic Tree
dbd

Probability Density Under Birth--Death Models
zoom

Zoom on a Portion of a Phylogeny
is.compatible

Check Compatibility of Splits
bird.orders

Phylogeny of the Orders of Birds From Sibley and Ahlquist
plot.phylo

Plot Phylogenies
FastME

Tree Estimation Based on the Minimum Evolution Algorithm
chiroptera

Bat Phylogeny
mat3

Three Matrices
skyline

Skyline Plot Estimate of Effective Population Size
c.phylo

Building Lists of Trees
rotate

Swapping sister clades
ace

Ancestral Character Estimation
delta.plot

Delta Plots
corPagel

Pagel's ``lambda'' Correlation Structure
ltt.plot

Lineages Through Time Plot
triangMtd

Tree Reconstruction Based on the Triangles Method
yule

Fits the Yule Model to a Phylogenetic Tree
mcconwaysims.test

McConway-Sims Test of Homogeneous Diversification
compar.lynch

Lynch's Comparative Method
nodelabels

Labelling the Nodes, Tips, and Edges of a Tree
corMartins

Martins's (1997) Correlation Structure
write.tree

Write Tree File in Parenthetic Format
identify.phylo

Graphical Identification of Nodes and Tips
bind.tree

Binds Trees
compute.brtime

Compute and Set Branching Times
corBrownian

Brownian Correlation Structure
drop.tip

Remove Tips in a Phylogenetic Tree
pic

Phylogenetically Independent Contrasts
mvr

Minimum Variance Reduction
richness.yule.test

Test of Diversification-Shift With the Yule Process
edges

Draw Additional Edges on a Plotted Tree
trex

Tree Explorer With Multiple Devices
rTraitMult

Multivariate Character Simulation
subtreeplot

Zoom on a Portion of a Phylogeny by Successive Clicks
read.tree

Read Tree File in Parenthetic Format
root

Roots Phylogenetic Trees
dist.dna

Pairwise Distances from DNA Sequences
bd.time

Time-Dependent Birth-Death Models
rTraitDisc

Discrete Character Simulation
diversity.contrast.test

Diversity Contrast Test
mst

Minimum Spanning Tree
howmanytrees

Calculate Numbers of Phylogenetic Trees
pcoa

Principal Coordinate Analysis
evonet

Evolutionary Networks
compar.ou

Ornstein--Uhlenbeck Model for Continuous Characters
mcmc.popsize

Reversible Jump MCMC to Infer Demographic History
lmorigin

Multiple regression through the origin
rlineage

Tree Simulation Under the Time-Dependent Birth--Death Models
yule.cov

Fits the Yule Model With Covariates
compute.brlen

Branch Lengths Computation
phymltest

Fits a Bunch of Models with PhyML
mat5Mrand

Five Independent Trees
parafit

Test of host-parasite coevolution