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ape (version 2.7-3)

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, analyses of diversification and macroevolution, computing distances from allelic and nucleotide data, reading nucleotide sequences, and several tools such as Mantel's test, computation of minimum spanning tree, generalized skyline plots, estimation of absolute evolutionary rates and clock-like trees using mean path lengths, non-parametric rate smoothing and penalized likelihood. Phylogeny estimation can be done with the NJ, BIONJ, and ME methods.

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Version

Install

install.packages('ape')

Monthly Downloads

84,031

Version

2.7-3

License

GPL (>= 2)

Maintainer

Emmanuel Paradis

Last Published

August 9th, 2011

Functions in ape (2.7-3)

rTraitDisc

Discrete Character Simulation
MPR

Most Parsimonious Reconstruction
read.nexus.data

Read Character Data In NEXUS Format
compute.brlen

Branch Lengths Computation
cophenetic.phylo

Pairwise Distances from a Phylogenetic Tree
bird.orders

Phylogeny of the Orders of Birds From Sibley and Ahlquist
chiroptera

Bat Phylogeny
compar.cheverud

Cheverud's Comparative Method
as.matching

Conversion Between Phylo and Matching Objects
Initialize.corPhyl

Initialize a `corPhyl' Structure Object
base.freq

Base frequencies from DNA Sequences
corBrownian

Brownian Correlation Structure
ape-internal

Internal Ape Functions
as.phylo.formula

Conversion from Taxonomy Variables to Phylogenetic Trees
birthdeath

Estimation of Speciation and Extinction Rates With Birth-Death Models
ape-defunct

Defunct Ape Functions
cherry

Number of Cherries and Null Models of Trees
compar.gee

Comparative Analysis with GEEs
corBlomberg

Blomberg et al.'s Correlation Structure
bd.ext

Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
coalescent.intervals

Coalescent Intervals
cophyloplot

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

Grafen's (1989) Correlation Structure
axisPhylo

Axis on Side of Phylogeny
is.monophyletic

Is Group Monophyletic
c.phylo

Building Lists of Trees
chronoMPL

Molecular Dating With Mean Path Lengths
image.DNAbin

Plot of DNA Sequence Alignement
compar.lynch

Lynch's Comparative Method
bind.tree

Binds Trees
howmanytrees

Calculate Numbers of Phylogenetic Trees
balance

Balance of a Dichotomous Phylogenetic Tree
add.scale.bar

Add a Scale Bar to a Phylogeny Plot
as.phylo

Conversion Among Tree and Network Objects
mcconwaysims.test

McConway-Sims Test of Homogeneous Diversification
node.depth

Depth of Nodes and Tips
reorder.phylo

Internal Reordering of Trees
read.GenBank

Read DNA Sequences from GenBank via Internet
corClasses

Phylogenetic Correlation Structures
clustal

Multiple Sequence Alignment with External Applications
diversity.contrast.test

Diversity Contrast Test
kronoviz

Plot Multiple Chronograms on the Same Scale
plot.varcomp

Plot Variance Components
identify.phylo

Graphical Identification of Nodes and Tips
mrca

Find Most Recent Common Ancestors Between Pairs
opsin

Gene Tree of 32 opsin Sequences
all.equal.phylo

Global Comparison of two Phylogenies
zoom

Zoom on a Portion of a Phylogeny
bird.families

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

Mantel Test for Similarity of Two Matrices
collapsed.intervals

Collapsed Coalescent Intervals
makeLabel

Label Management
dist.gene

Pairwise Distances from Genetic Data
subtrees

All subtrees of a Phylogenetic Tree
write.dna

Write DNA Sequences in a File
lmorigin

Multiple regression through the origin
subtreeplot

Zoom on a Portion of a Phylogeny by Successive Clicks
mst

Minimum Spanning Tree
mat5M3ID

Five Trees
diversi.gof

Tests of Constant Diversification Rates
GC.content

Content in GC from DNA Sequences
yule

Fits the Yule Model to a Phylogenetic Tree
varcomp

Compute Variance Component Estimates
nodelabels

Labelling the Nodes, Tips, and Edges of a Tree
read.tree

Read Tree File in Parenthetic Format
gammaStat

Gamma-Statistic of Pybus and Harvey
is.ultrametric

Test if a Tree is Ultrametric
slowinskiguyer.test

Slowinski-Guyer Test of Homogeneous Diversification
unique.multiPhylo

Revomes Duplicate Trees
read.caic

Read Tree File in CAIC Format
phymltest

Fits a Bunch of Models with PhyML
FastME

Tree Estimation Based on the Minimum Evolution Algorithm
skyline

Skyline Plot Estimate of Effective Population Size
rotate

Swapping sister clades
mat3

Three Matrices
delta.plot

Delta Plots
seg.sites

Find Segregating Sites in DNA Sequences
landplants

Gene Tree of 36 Landplant rbcL Sequences
evonet

Evolutionary Networks
del.gaps

Delete Alignment Gaps in DNA Sequences
write.tree

Write Tree File in Parenthetic Format
print.phylo

Compact Display of a Phylogeny
write.nexus

Write Tree File in Nexus Format
Moran.I

Moran's I Autocorrelation Index
skylineplot

Drawing Skyline Plot Graphs
read.dna

Read DNA Sequences in a File
richness.yule.test

Test of Diversification-Shift With the Yule Process
as.alignment

Conversion Among DNA Sequence Internal Formats
chronopl

Molecular Dating With Penalized Likelihood
ltt.plot

Lineages Through Time Plot
makeNodeLabel

Makes Node Labels
which.edge

Identifies Edges of a Tree
pcoa

Principal Coordinate Analysis
varCompPhylip

Variance Components with Orthonormal Contrasts
root

Roots Phylogenetic Trees
DNAbin

Manipulate DNA Sequences in Bit-Level Format
data.nex

NEXUS Data Example
speciesTree

Species Tree Estimation
ace

Ancestral Character Estimation
parafit

Test of host-parasite coevolution
nj

Neighbor-Joining Tree Estimation
plot.phylo

Plot Phylogenies
dist.topo

Topological Distances Between Two Trees
corMartins

Martins's (1997) Correlation Structure
stree

Generates Systematic Regular Trees
diversi.time

Analysis of Diversification with Survival Models
compar.ou

Ornstein--Uhlenbeck Model for Continuous Characters
summary.phylo

Print Summary of a Phylogeny
multi2di

Collapse and Resolve Multichotomies
BIONJ

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

Carnivora body sizes and life history traits
correlogram.formula

Phylogenetic Correlogram
woodmouse

Cytochrome b Gene Sequences of Woodmice
yule.cov

Fits the Yule Model With Covariates
branching.times

Branching Times of a Phylogenetic Tree
mcmc.popsize

Reversible Jump MCMC to Infer Demographic History
pic

Phylogenetically Independent Contrasts
ladderize

Ladderize a Tree
vcv

Phylogenetic Variance-covariance or Correlation Matrix
consensus

Concensus Trees
compute.brtime

Compute and Set Branching Times
trex

Tree Explorer With Multiple Devices
is.binary.tree

Test for Binary Tree
multiphylo

Manipulating Lists of Trees
bd.time

Time-Dependent Birth-Death Models
pic.ortho

Phylogenetically Independent Orthonormal Contrasts
mat5Mrand

Five Independent Trees
CADM.global

Congruence among distance matrices
rlineage

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

Matrix Exponential
rtree

Generates Random Trees
weight.taxo

Define Similarity Matrix
ape-package

Analyses of Phylogenetics and Evolution
yule.time

Fits the Time-Dependent Yule Model
corPagel

Pagel's ``lambda'' Correlation Structure
read.nexus

Read Tree File in Nexus Format
edges

Draw Additional Edges on a Plotted Tree
collapse.singles

Collapse Single Nodes
rTraitMult

Multivariate Character Simulation
boot.phylo

Tree Bipartition and Bootstrapping Phylogenies
hivtree

Phylogenetic Tree of 193 HIV-1 Sequences
mixedFontLabel

Mixed Font Labels for Plotting
rTraitCont

Continuous Character Simulation
dist.dna

Pairwise Distances from DNA Sequences
write.nexus.data

Write Character Data In NEXUS Format
plot.correlogram

Plot a Correlogram
drop.tip

Remove Tips in a Phylogenetic Tree