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ape (version 3.1-1)

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, 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

87,302

Version

3.1-1

License

GPL (>= 2)

Maintainer

Emmanuel Paradis

Last Published

March 11th, 2014

Functions in ape (3.1-1)

additive

Incomplete Distance Matrix Filling
mat5M3ID

Five Trees
lmorigin

Multiple regression through the origin
compar.cheverud

Cheverud's Comparative Method
as.alignment

Conversion Among DNA Sequence Internal Formats
add.scale.bar

Add a Scale Bar to a Phylogeny Plot
corGrafen

Grafen's (1989) Correlation Structure
balance

Balance of a Dichotomous Phylogenetic Tree
read.nexus.data

Read Character Data In NEXUS Format
is.compatible

Check Compatibility of Splits
nj

Neighbor-Joining Tree Estimation
all.equal.phylo

Global Comparison of two Phylogenies
is.monophyletic

Is Group Monophyletic
base.freq

Base frequencies from DNA Sequences
gammaStat

Gamma-Statistic of Pybus and Harvey
multi2di

Collapse and Resolve Multichotomies
birthdeath

Estimation of Speciation and Extinction Rates With Birth-Death Models
as.phylo.formula

Conversion from Taxonomy Variables to Phylogenetic Trees
chronoMPL

Molecular Dating With Mean Path Lengths
plot.correlogram

Plot a Correlogram
consensus

Concensus Trees
BIONJ

Tree Estimation Based on an Improved Version of the NJ Algorithm
delta.plot

Delta Plots
phydataplot

Tree Annotation
root

Roots Phylogenetic Trees
MPR

Most Parsimonious Reconstruction
bird.orders

Phylogeny of the Orders of Birds From Sibley and Ahlquist
mantel.test

Mantel Test for Similarity of Two Matrices
correlogram.formula

Phylogenetic Correlogram
dbd

Probability Density Under Birth--Death Models
Moran.I

Moran's I Autocorrelation Index
DNAbin

Manipulate DNA Sequences in Bit-Level Format
edges

Draw Additional Edges on a Plotted Tree
as.matching

Conversion Between Phylo and Matching Objects
cherry

Number of Cherries and Null Models of Trees
bind.tree

Binds Trees
ace

Ancestral Character Estimation
axisPhylo

Axis on Side of Phylogeny
diversi.gof

Tests of Constant Diversification Rates
clustal

Multiple Sequence Alignment with External Applications
bd.time

Time-Dependent Birth-Death Models
nodelabels

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

Blomberg et al.'s Correlation Structure
chronopl

Molecular Dating With Penalized Likelihood
rTraitDisc

Discrete Character Simulation
ladderize

Ladderize a Tree
diversi.time

Analysis of Diversification with Survival Models
collapsed.intervals

Collapsed Coalescent Intervals
dist.dna

Pairwise Distances from DNA Sequences
rTraitMult

Multivariate Character Simulation
makeLabel

Label Management
del.gaps

Delete Alignment Gaps in DNA Sequences
corClasses

Phylogenetic Correlation Structures
mixedFontLabel

Mixed Font Labels for Plotting
ewLasso

Incomplete distances and edge weights of unrooted topology
summary.phylo

Print Summary of a Phylogeny
drop.tip

Remove Tips in a Phylogenetic Tree
diversity.contrast.test

Diversity Contrast Test
rlineage

Tree Simulation Under the Time-Dependent Birth--Death Models
dist.gene

Pairwise Distances from Genetic Data
cophenetic.phylo

Pairwise Distances from a Phylogenetic Tree
write.nexus.data

Write Character Data in NEXUS Format
ape-internal

Internal Ape Functions
triangMtd

Tree Reconstruction Based on the Triangles Method
compute.brtime

Compute and Set Branching Times
FastME

Tree Estimation Based on the Minimum Evolution Algorithm
carnivora

Carnivora body sizes and life history traits
reorder.phylo

Internal Reordering of Trees
slowinskiguyer.test

Slowinski-Guyer Test of Homogeneous Diversification
corPagel

Pagel's ``lambda'' Correlation Structure
LTT

Theoretical Lineage-Through Time Plots
corBrownian

Brownian Correlation Structure
woodmouse

Cytochrome b Gene Sequences of Woodmice
rotate

Swapping Sister Clades
chiroptera

Bat Phylogeny
chronos

Molecular Dating by Penalised Likelihood and Maximum Likelihood
bird.families

Phylogeny of the Families of Birds From Sibley and Ahlquist
rTraitCont

Continuous Character Simulation
read.caic

Read Tree File in CAIC Format
parafit

Test of host-parasite coevolution
is.binary.tree

Test for Binary Tree
compar.gee

Comparative Analysis with GEEs
yule

Fits the Yule Model to a Phylogenetic Tree
c.phylo

Building Lists of Trees
matexpo

Matrix Exponential
compar.ou

Ornstein--Uhlenbeck Model for Continuous Characters
is.ultrametric

Test if a Tree is Ultrametric
print.phylo

Compact Display of a Phylogeny
cophyloplot

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

Read Tree File in Nexus Format
bd.ext

Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
collapse.singles

Collapse Single Nodes
corMartins

Martins's (1997) Correlation Structure
mat5Mrand

Five Independent Trees
coalescent.intervals

Coalescent Intervals
vcv

Phylogenetic Variance-covariance or Correlation Matrix
ltt.plot

Lineages Through Time Plot
zoom

Zoom on a Portion of a Phylogeny
makeNodeLabel

Makes Node Labels
speciesTree

Species Tree Estimation
mrca

Find Most Recent Common Ancestors Between Pairs
unique.multiPhylo

Revomes Duplicate Trees
yule.time

Fits the Time-Dependent Yule Model
multiphylo

Manipulating Lists of Trees
read.dna

Read DNA Sequences in a File
varcomp

Compute Variance Component Estimates
write.dna

Write DNA Sequences in a File
as.bitsplits

Split Frequencies and Conversion Among Split Classes
where

Find Patterns in DNA Sequences
treePop

Tree Popping
which.edge

Identifies Edges of a Tree
opsin

Gene Tree of 32 opsin Sequences
rtree

Generates Random Trees
richness.yule.test

Test of Diversification-Shift With the Yule Process
yule.cov

Fits the Yule Model With Covariates
plot.varcomp

Plot Variance Components
skyline

Skyline Plot Estimate of Effective Population Size
stree

Generates Systematic Regular Trees
data.nex

NEXUS Data Example
hivtree

Phylogenetic Tree of 193 HIV-1 Sequences
mcconwaysims.test

McConway-Sims Test of Homogeneous Diversification
write.tree

Write Tree File in Parenthetic Format
write.nexus

Write Tree File in Nexus Format
evonet

Evolutionary Networks
pic

Phylogenetically Independent Contrasts
landplants

Gene Tree of 36 Landplant rbcL Sequences
identify.phylo

Graphical Identification of Nodes and Tips
mcmc.popsize

Reversible Jump MCMC to Infer Demographic History
read.tree

Read Tree File in Parenthetic Format
mat3

Three Matrices
CADM.global

Congruence among distance matrices
pcoa

Principal Coordinate Analysis
pic.ortho

Phylogenetically Independent Orthonormal Contrasts
Initialize.corPhyl

Initialize a `corPhyl' Structure Object
boot.phylo

Tree Bipartition and Bootstrapping Phylogenies
weight.taxo

Define Similarity Matrix
subtrees

All subtrees of a Phylogenetic Tree
as.phylo

Conversion Among Tree and Network Objects
seg.sites

Find Segregating Sites in DNA Sequences
subtreeplot

Zoom on a Portion of a Phylogeny by Successive Clicks
branching.times

Branching Times of a Phylogenetic Tree
ape-package

Analyses of Phylogenetics and Evolution
dist.topo

Topological Distances Between Two Trees
howmanytrees

Calculate Numbers of Phylogenetic Trees
image.DNAbin

Plot of DNA Sequence Alignement
kronoviz

Plot Multiple Chronograms on the Same Scale
compute.brlen

Branch Lengths Computation
plot.phylo

Plot Phylogenies
read.GenBank

Read DNA Sequences from GenBank via Internet
mst

Minimum Spanning Tree
node.depth

Depth and Heights of Nodes and Tips
skylineplot

Drawing Skyline Plot Graphs
njs

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

Fits a Bunch of Models with PhyML
mvr

Minimum Variance Reduction
SDM

Construction of Consensus Distance Matrix With SDM
alex

Alignment Explorer With Multiple Devices
trex

Tree Explorer With Multiple Devices
varCompPhylip

Variance Components with Orthonormal Contrasts
compar.lynch

Lynch's Comparative Method
rtt

Root a Tree by Root-to-Tip Regression