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ape (version 3.0-11)

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

3.0-11

License

GPL (>= 2)

Maintainer

Emmanuel Paradis

Last Published

October 1st, 2013

Functions in ape (3.0-11)

dist.gene

Pairwise Distances from Genetic Data
as.bitsplits

Conversion Among Split Classes
as.alignment

Conversion Among DNA Sequence Internal Formats
all.equal.phylo

Global Comparison of two Phylogenies
base.freq

Base frequencies from DNA Sequences
MPR

Most Parsimonious Reconstruction
ape-internal

Internal Ape Functions
clustal

Multiple Sequence Alignment with External Applications
c.phylo

Building Lists of Trees
collapsed.intervals

Collapsed Coalescent Intervals
add.scale.bar

Add a Scale Bar to a Phylogeny Plot
corBlomberg

Blomberg et al.'s Correlation Structure
branching.times

Branching Times of a Phylogenetic Tree
corMartins

Martins's (1997) Correlation Structure
consensus

Concensus Trees
corPagel

Pagel's ``lambda'' Correlation Structure
corGrafen

Grafen's (1989) Correlation Structure
compar.lynch

Lynch's Comparative Method
is.binary.tree

Test for Binary Tree
alex

Alignment Explorer With Multiple Devices
multi2di

Collapse and Resolve Multichotomies
chronos

Molecular Dating by Penalised Likelihood and Maximum Likelihood
data.nex

NEXUS Data Example
kronoviz

Plot Multiple Chronograms on the Same Scale
as.matching

Conversion Between Phylo and Matching Objects
Moran.I

Moran's I Autocorrelation Index
ewLasso

Incomplete distances and edge weights of unrooted topology
axisPhylo

Axis on Side of Phylogeny
mat3

Three Matrices
is.monophyletic

Is Group Monophyletic
identify.phylo

Graphical Identification of Nodes and Tips
njs

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

Incomplete Distance Matrix Filling
gammaStat

Gamma-Statistic of Pybus and Harvey
mvr

Minimum Variance Reduction
print.phylo

Compact Display of a Phylogeny
mat5M3ID

Five Trees
hivtree

Phylogenetic Tree of 193 HIV-1 Sequences
pic

Phylogenetically Independent Contrasts
CADM.global

Congruence among distance matrices
edges

Draw Additional Edges on a Plotted Tree
weight.taxo

Define Similarity Matrix
pic.ortho

Phylogenetically Independent Orthonormal Contrasts
trex

Tree Explorer With Multiple Devices
rTraitCont

Continuous Character Simulation
slowinskiguyer.test

Slowinski-Guyer Test of Homogeneous Diversification
dbd

Probability Density Under Birth--Death Models
dist.topo

Topological Distances Between Two Trees
opsin

Gene Tree of 32 opsin Sequences
boot.phylo

Tree Bipartition and Bootstrapping Phylogenies
cophenetic.phylo

Pairwise Distances from a Phylogenetic Tree
is.compatible

Check Compatibility of Splits
bird.families

Phylogeny of the Families of Birds From Sibley and Ahlquist
collapse.singles

Collapse Single Nodes
Initialize.corPhyl

Initialize a `corPhyl' Structure Object
compar.gee

Comparative Analysis with GEEs
del.gaps

Delete Alignment Gaps in DNA Sequences
compar.ou

Ornstein--Uhlenbeck Model for Continuous Characters
mcmc.popsize

Reversible Jump MCMC to Infer Demographic History
bd.ext

Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
as.phylo.formula

Conversion from Taxonomy Variables to Phylogenetic Trees
delta.plot

Delta Plots
is.ultrametric

Test if a Tree is Ultrametric
compute.brtime

Compute and Set Branching Times
corBrownian

Brownian Correlation Structure
dist.dna

Pairwise Distances from DNA Sequences
read.nexus

Read Tree File in Nexus Format
makeNodeLabel

Makes Node Labels
rTraitDisc

Discrete Character Simulation
diversi.time

Analysis of Diversification with Survival Models
varcomp

Compute Variance Component Estimates
which.edge

Identifies Edges of a Tree
chronopl

Molecular Dating With Penalized Likelihood
triangMtd

Tree Reconstruction Based on the Triangles Method
compute.brlen

Branch Lengths Computation
ape-package

Analyses of Phylogenetics and Evolution
mat5Mrand

Five Independent Trees
where

Find Patterns in DNA Sequences
diversity.contrast.test

Diversity Contrast Test
birthdeath

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

Matrix Exponential
summary.phylo

Print Summary of a Phylogeny
howmanytrees

Calculate Numbers of Phylogenetic Trees
read.tree

Read Tree File in Parenthetic Format
diversi.gof

Tests of Constant Diversification Rates
compar.cheverud

Cheverud's Comparative Method
evonet

Evolutionary Networks
skylineplot

Drawing Skyline Plot Graphs
BIONJ

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

Tree Simulation Under the Time-Dependent Birth--Death Models
subtreeplot

Zoom on a Portion of a Phylogeny by Successive Clicks
unique.multiPhylo

Revomes Duplicate Trees
ace

Ancestral Character Estimation
plot.varcomp

Plot Variance Components
read.caic

Read Tree File in CAIC Format
write.tree

Write Tree File in Parenthetic Format
richness.yule.test

Test of Diversification-Shift With the Yule Process
skyline

Skyline Plot Estimate of Effective Population Size
plot.correlogram

Plot a Correlogram
bd.time

Time-Dependent Birth-Death Models
cophyloplot

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

Manipulating Lists of Trees
rotate

Swapping Sister Clades
corClasses

Phylogenetic Correlation Structures
mst

Minimum Spanning Tree
bind.tree

Binds Trees
as.phylo

Conversion Among Tree and Network Objects
yule.cov

Fits the Yule Model With Covariates
rTraitMult

Multivariate Character Simulation
root

Roots Phylogenetic Trees
lmorigin

Multiple regression through the origin
nj

Neighbor-Joining Tree Estimation
ladderize

Ladderize a Tree
seg.sites

Find Segregating Sites in DNA Sequences
treePop

Tree Popping
zoom

Zoom on a Portion of a Phylogeny
write.nexus.data

Write Character Data in NEXUS Format
yule.time

Fits the Time-Dependent Yule Model
mcconwaysims.test

McConway-Sims Test of Homogeneous Diversification
mrca

Find Most Recent Common Ancestors Between Pairs
SDM

Construction of Consensus Distance Matrix With SDM
speciesTree

Species Tree Estimation
bird.orders

Phylogeny of the Orders of Birds From Sibley and Ahlquist
woodmouse

Cytochrome b Gene Sequences of Woodmice
write.nexus

Write Tree File in Nexus Format
chiroptera

Bat Phylogeny
mantel.test

Mantel Test for Similarity of Two Matrices
balance

Balance of a Dichotomous Phylogenetic Tree
correlogram.formula

Phylogenetic Correlogram
carnivora

Carnivora body sizes and life history traits
drop.tip

Remove Tips in a Phylogenetic Tree
landplants

Gene Tree of 36 Landplant rbcL Sequences
cherry

Number of Cherries and Null Models of Trees
phymltest

Fits a Bunch of Models with PhyML
plot.phylo

Plot Phylogenies
subtrees

All subtrees of a Phylogenetic Tree
image.DNAbin

Plot of DNA Sequence Alignement
varCompPhylip

Variance Components with Orthonormal Contrasts
read.GenBank

Read DNA Sequences from GenBank via Internet
reorder.phylo

Internal Reordering of Trees
parafit

Test of host-parasite coevolution
ltt.plot

Lineages Through Time Plot
nodelabels

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

Phylogenetic Variance-covariance or Correlation Matrix
makeLabel

Label Management
mixedFontLabel

Mixed Font Labels for Plotting
read.dna

Read DNA Sequences in a File
node.depth

Depth and Heights of Nodes and Tips
read.nexus.data

Read Character Data In NEXUS Format
write.dna

Write DNA Sequences in a File
rtree

Generates Random Trees
FastME

Tree Estimation Based on the Minimum Evolution Algorithm
yule

Fits the Yule Model to a Phylogenetic Tree
DNAbin

Manipulate DNA Sequences in Bit-Level Format
pcoa

Principal Coordinate Analysis
chronoMPL

Molecular Dating With Mean Path Lengths
stree

Generates Systematic Regular Trees
coalescent.intervals

Coalescent Intervals