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ape (version 3.0-7)

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

87,302

Version

3.0-7

License

GPL (>= 2)

Maintainer

Emmanuel Paradis

Last Published

January 21st, 2013

Functions in ape (3.0-7)

collapsed.intervals

Collapsed Coalescent Intervals
corClasses

Phylogenetic Correlation Structures
as.phylo

Conversion Among Tree and Network Objects
Initialize.corPhyl

Initialize a `corPhyl' Structure Object
all.equal.phylo

Global Comparison of two Phylogenies
bind.tree

Binds Trees
ladderize

Ladderize a Tree
balance

Balance of a Dichotomous Phylogenetic Tree
coalescent.intervals

Coalescent Intervals
correlogram.formula

Phylogenetic Correlogram
Moran.I

Moran's I Autocorrelation Index
bird.orders

Phylogeny of the Orders of Birds From Sibley and Ahlquist
bd.time

Time-Dependent Birth-Death Models
birthdeath

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

Draw Additional Edges on a Plotted Tree
branching.times

Branching Times of a Phylogenetic Tree
corMartins

Martins's (1997) Correlation Structure
axisPhylo

Axis on Side of Phylogeny
plot.varcomp

Plot Variance Components
mrca

Find Most Recent Common Ancestors Between Pairs
rTraitMult

Multivariate Character Simulation
alex

Alignment Explorer With Multiple Devices
seg.sites

Find Segregating Sites in DNA Sequences
FastME

Tree Estimation Based on the Minimum Evolution Algorithm
compute.brtime

Compute and Set Branching Times
read.nexus.data

Read Character Data In NEXUS Format
compar.cheverud

Cheverud's Comparative Method
BIONJ

Tree Estimation Based on an Improved Version of the NJ Algorithm
read.nexus

Read Tree File in Nexus Format
consensus

Concensus Trees
bird.families

Phylogeny of the Families of Birds From Sibley and Ahlquist
ace

Ancestral Character Estimation
print.phylo

Compact Display of a Phylogeny
varcomp

Compute Variance Component Estimates
is.compatible

Check Compatibility of Splits
rTraitDisc

Discrete Character Simulation
rlineage

Tree Simulation Under the Time-Dependent Birth--Death Models
mat3

Three Matrices
matexpo

Matrix Exponential
cophenetic.phylo

Pairwise Distances from a Phylogenetic Tree
data.nex

NEXUS Data Example
ape-internal

Internal Ape Functions
is.ultrametric

Test if a Tree is Ultrametric
additive

Incomplete Distance Matrix Filling
multiphylo

Manipulating Lists of Trees
mat5M3ID

Five Trees
as.matching

Conversion Between Phylo and Matching Objects
del.gaps

Delete Alignment Gaps in DNA Sequences
ltt.plot

Lineages Through Time Plot
as.bitsplits

Conversion Among Split Classes
mat5Mrand

Five Independent Trees
DNAbin

Manipulate DNA Sequences in Bit-Level Format
chiroptera

Bat Phylogeny
drop.tip

Remove Tips in a Phylogenetic Tree
is.binary.tree

Test for Binary Tree
read.caic

Read Tree File in CAIC Format
stree

Generates Systematic Regular Trees
rtree

Generates Random Trees
richness.yule.test

Test of Diversification-Shift With the Yule Process
MPR

Most Parsimonious Reconstruction
reorder.phylo

Internal Reordering of Trees
varCompPhylip

Variance Components with Orthonormal Contrasts
landplants

Gene Tree of 36 Landplant rbcL Sequences
base.freq

Base frequencies from DNA Sequences
kronoviz

Plot Multiple Chronograms on the Same Scale
image.DNAbin

Plot of DNA Sequence Alignement
treePop

Tree Popping
triangMtd

Tree Reconstruction Based on the Triangles Method
trex

Tree Explorer With Multiple Devices
collapse.singles

Collapse Single Nodes
howmanytrees

Calculate Numbers of Phylogenetic Trees
compar.ou

Ornstein--Uhlenbeck Model for Continuous Characters
diversity.contrast.test

Diversity Contrast Test
corBlomberg

Blomberg et al.'s Correlation Structure
read.dna

Read DNA Sequences in a File
read.tree

Read Tree File in Parenthetic Format
mvr

Minimum Variance Reduction
clustal

Multiple Sequence Alignment with External Applications
rTraitCont

Continuous Character Simulation
bd.ext

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

Brownian Correlation Structure
summary.phylo

Print Summary of a Phylogeny
rotate

Swapping sister clades
identify.phylo

Graphical Identification of Nodes and Tips
compute.brlen

Branch Lengths Computation
root

Roots Phylogenetic Trees
as.phylo.formula

Conversion from Taxonomy Variables to Phylogenetic Trees
mcconwaysims.test

McConway-Sims Test of Homogeneous Diversification
evonet

Evolutionary Networks
add.scale.bar

Add a Scale Bar to a Phylogeny Plot
compar.lynch

Lynch's Comparative Method
mixedFontLabel

Mixed Font Labels for Plotting
makeLabel

Label Management
gammaStat

Gamma-Statistic of Pybus and Harvey
corGrafen

Grafen's (1989) Correlation Structure
subtreeplot

Zoom on a Portion of a Phylogeny by Successive Clicks
mantel.test

Mantel Test for Similarity of Two Matrices
corPagel

Pagel's ``lambda'' Correlation Structure
yule

Fits the Yule Model to a Phylogenetic Tree
ape-package

Analyses of Phylogenetics and Evolution
subtrees

All subtrees of a Phylogenetic Tree
as.alignment

Conversion Among DNA Sequence Internal Formats
vcv

Phylogenetic Variance-covariance or Correlation Matrix
c.phylo

Building Lists of Trees
SDM

Construction of Consensus Distance Matrix With SDM
boot.phylo

Tree Bipartition and Bootstrapping Phylogenies
cophyloplot

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

Molecular Dating With Mean Path Lengths
compar.gee

Comparative Analysis with GEEs
mcmc.popsize

Reversible Jump MCMC to Infer Demographic History
read.GenBank

Read DNA Sequences from GenBank via Internet
skylineplot

Drawing Skyline Plot Graphs
makeNodeLabel

Makes Node Labels
which.edge

Identifies Edges of a Tree
opsin

Gene Tree of 32 opsin Sequences
speciesTree

Species Tree Estimation
weight.taxo

Define Similarity Matrix
dist.gene

Pairwise Distances from Genetic Data
nj

Neighbor-Joining Tree Estimation
write.nexus

Write Tree File in Nexus Format
unique.multiPhylo

Revomes Duplicate Trees
multi2di

Collapse and Resolve Multichotomies
mst

Minimum Spanning Tree
CADM.global

Congruence among distance matrices
write.nexus.data

Write Character Data In NEXUS Format
diversi.time

Analysis of Diversification with Survival Models
dbd

Probability Density Under Birth--Death Models
write.dna

Write DNA Sequences in a File
parafit

Test of host-parasite coevolution
skyline

Skyline Plot Estimate of Effective Population Size
chronos

Molecular Dating by Penalised Likelihood and Maximum Likelihood
yule.cov

Fits the Yule Model With Covariates
woodmouse

Cytochrome b Gene Sequences of Woodmice
phymltest

Fits a Bunch of Models with PhyML
lmorigin

Multiple regression through the origin
pic.ortho

Phylogenetically Independent Orthonormal Contrasts
plot.phylo

Plot Phylogenies
delta.plot

Delta Plots
dist.topo

Topological Distances Between Two Trees
diversi.gof

Tests of Constant Diversification Rates
plot.correlogram

Plot a Correlogram
zoom

Zoom on a Portion of a Phylogeny
node.depth

Depth and Heights of Nodes and Tips
pic

Phylogenetically Independent Contrasts
yule.time

Fits the Time-Dependent Yule Model
njs

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

Find Patterns in DNA Sequences
write.tree

Write Tree File in Parenthetic Format
dist.dna

Pairwise Distances from DNA Sequences
pcoa

Principal Coordinate Analysis
cherry

Number of Cherries and Null Models of Trees
is.monophyletic

Is Group Monophyletic
slowinskiguyer.test

Slowinski-Guyer Test of Homogeneous Diversification
carnivora

Carnivora body sizes and life history traits
chronopl

Molecular Dating With Penalized Likelihood
hivtree

Phylogenetic Tree of 193 HIV-1 Sequences
nodelabels

Labelling the Nodes, Tips, and Edges of a Tree