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ape (version 3.2)

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 as well as importing from BioConductor, 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

84,031

Version

3.2

License

GPL (>= 2)

Maintainer

Emmanuel Paradis

Last Published

December 5th, 2014

Functions in ape (3.2)

as.alignment

Conversion Among DNA Sequence Internal Formats
carnivora

Carnivora body sizes and life history traits
makeLabel

Label Management
c.phylo

Building Lists of Trees
corPagel

Pagel's ``lambda'' Correlation Structure
compar.gee

Comparative Analysis with GEEs
DNAbin

Manipulate DNA Sequences in Bit-Level Format
diversi.gof

Tests of Constant Diversification Rates
as.phylo

Conversion Among Tree and Network Objects
chronoMPL

Molecular Dating With Mean Path Lengths
njs

Tree Reconstruction from Incomplete Distances With NJ* or bio-NJ*
write.tree

Write Tree File in Parenthetic Format
ape-package

Analyses of Phylogenetics and Evolution
MPR

Most Parsimonious Reconstruction
mcmc.popsize

Reversible Jump MCMC to Infer Demographic History
mat5M3ID

Five Trees
mat5Mrand

Five Independent Trees
corClasses

Phylogenetic Correlation Structures
plot.varcomp

Plot Variance Components
delta.plot

Delta Plots
stree

Generates Systematic Regular Trees
nodelabels

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

Species Tree Estimation
cherry

Number of Cherries and Null Models of Trees
SDM

Construction of Consensus Distance Matrix With SDM
compar.ou

Ornstein--Uhlenbeck Model for Continuous Characters
is.binary.tree

Test for Binary Tree
cophyloplot

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

Tree Bipartition and Bootstrapping Phylogenies
subtrees

All subtrees of a Phylogenetic Tree
CADM.global

Congruence among distance matrices
branching.times

Branching Times of a Phylogenetic Tree
mixedFontLabel

Mixed Font Labels for Plotting
mst

Minimum Spanning Tree
phymltest

Fits a Bunch of Models with PhyML
opsin

Gene Tree of 32 opsin Sequences
matexpo

Matrix Exponential
def

Definition of Vectors for Plotting or Annotating
edges

Draw Additional Edges on a Plotted Tree
as.matching

Conversion Between Phylo and Matching Objects
weight.taxo

Define Similarity Matrix
mvr

Minimum Variance Reduction
bird.orders

Phylogeny of the Orders of Birds From Sibley and Ahlquist
dist.dna

Pairwise Distances from DNA Sequences
mantel.test

Mantel Test for Similarity of Two Matrices
ace

Ancestral Character Estimation
del.gaps

Delete Alignment Gaps in DNA Sequences
nodepath

Find Paths of Nodes
alex

Alignment Explorer With Multiple Devices
mrca

Find Most Recent Common Ancestors Between Pairs
kronoviz

Plot Multiple Chronograms on the Same Scale
richness.yule.test

Test of Diversification-Shift With the Yule Process
ape-internal

Internal Ape Functions
plot.correlogram

Plot a Correlogram
base.freq

Base frequencies from DNA Sequences
rtree

Generates Random Trees
chronos

Molecular Dating by Penalised Likelihood and Maximum Likelihood
corBrownian

Brownian Correlation Structure
landplants

Gene Tree of 36 Landplant rbcL Sequences
rTraitCont

Continuous Character Simulation
Initialize.corPhyl

Initialize a `corPhyl' Structure Object
data.nex

NEXUS Data Example
zoom

Zoom on a Portion of a Phylogeny
howmanytrees

Calculate Numbers of Phylogenetic Trees
reorder.phylo

Internal Reordering of Trees
diversity.contrast.test

Diversity Contrast Test
varcomp

Compute Variance Component Estimates
rTraitDisc

Discrete Character Simulation
lmorigin

Multiple regression through the origin
write.dna

Write DNA Sequences in a File
root

Roots Phylogenetic Trees
slowinskiguyer.test

Slowinski-Guyer Test of Homogeneous Diversification
skylineplot

Drawing Skyline Plot Graphs
is.ultrametric

Test if a Tree is Ultrametric
trex

Tree Explorer With Multiple Devices
mcconwaysims.test

McConway-Sims Test of Homogeneous Diversification
woodmouse

Cytochrome b Gene Sequences of Woodmice
write.nexus

Write Tree File in Nexus Format
node.depth

Depth and Heights of Nodes and Tips
nj

Neighbor-Joining Tree Estimation
rotate

Swapping Sister Clades
plot.phylo

Plot Phylogenies
rTraitMult

Multivariate Character Simulation
vcv

Phylogenetic Variance-covariance or Correlation Matrix
consensus

Concensus Trees
gammaStat

Gamma-Statistic of Pybus and Harvey
compar.cheverud

Cheverud's Comparative Method
compar.lynch

Lynch's Comparative Method
identify.phylo

Graphical Identification of Nodes and Tips
dbd

Probability Density Under Birth--Death Models
ltt.plot

Lineages Through Time Plot
mat3

Three Matrices
pic.ortho

Phylogenetically Independent Orthonormal Contrasts
axisPhylo

Axis on Side of Phylogeny
read.nexus.data

Read Character Data In NEXUS Format
seg.sites

Find Segregating Sites in DNA Sequences
hivtree

Phylogenetic Tree of 193 HIV-1 Sequences
varCompPhylip

Variance Components with Orthonormal Contrasts
write.nexus.data

Write Character Data in NEXUS Format
print.phylo

Compact Display of a Phylogeny
reconstruct

Continuous Ancestral Character Estimation
yule

Fits the Yule Model to a Phylogenetic Tree
Moran.I

Moran's I Autocorrelation Index
triangMtd

Tree Reconstruction Based on the Triangles Method
birthdeath

Estimation of Speciation and Extinction Rates With Birth-Death Models
bd.time

Time-Dependent Birth-Death Models
corGrafen

Grafen's (1989) Correlation Structure
yule.cov

Fits the Yule Model With Covariates
ladderize

Ladderize a Tree
BIONJ

Tree Estimation Based on an Improved Version of the NJ Algorithm
diversi.time

Analysis of Diversification with Survival Models
as.bitsplits

Split Frequencies and Conversion Among Split Classes
phydataplot

Tree Annotation
dist.topo

Topological Distances Between Two Trees
read.GenBank

Read DNA Sequences from GenBank via Internet
compute.brtime

Compute and Set Branching Times
correlogram.formula

Phylogenetic Correlogram
multiphylo

Manipulating Lists of Trees
balance

Balance of a Dichotomous Phylogenetic Tree
FastME

Tree Estimation Based on the Minimum Evolution Algorithm
is.monophyletic

Is Group Monophyletic
LTT

Theoretical Lineage-Through Time Plots
as.phylo.formula

Conversion from Taxonomy Variables to Phylogenetic Trees
treePop

Tree Popping
pcoa

Principal Coordinate Analysis
image.DNAbin

Plot of DNA Sequence Alignement
read.dna

Read DNA Sequences in a File
bind.tree

Binds Trees
bird.families

Phylogeny of the Families of Birds From Sibley and Ahlquist
unique.multiPhylo

Revomes Duplicate Trees
read.caic

Read Tree File in CAIC Format
read.tree

Read Tree File in Parenthetic Format
read.nexus

Read Tree File in Nexus Format
clustal

Multiple Sequence Alignment with External Applications
where

Find Patterns in DNA Sequences
yule.time

Fits the Time-Dependent Yule Model
collapsed.intervals

Collapsed Coalescent Intervals
rtt

Root a Tree by Root-to-Tip Regression
skyline

Skyline Plot Estimate of Effective Population Size
cophenetic.phylo

Pairwise Distances from a Phylogenetic Tree
which.edge

Identifies Edges of a Tree
rlineage

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

Phylogenetically Independent Contrasts
vcv2phylo

Variance-Covariance Matrix to Tree
summary.phylo

Print Summary of a Phylogeny
additive

Incomplete Distance Matrix Filling
all.equal.phylo

Global Comparison of two Phylogenies
add.scale.bar

Add a Scale Bar to a Phylogeny Plot
bd.ext

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

Molecular Dating With Penalized Likelihood
coalescent.intervals

Coalescent Intervals
compute.brlen

Branch Lengths Computation
dist.gene

Pairwise Distances from Genetic Data
ewLasso

Incomplete distances and edge weights of unrooted topology
multi2di

Collapse and Resolve Multichotomies
collapse.singles

Collapse Single Nodes
corBlomberg

Blomberg et al.'s Correlation Structure
makeNodeLabel

Makes Node Labels
chiroptera

Bat Phylogeny
corMartins

Martins's (1997) Correlation Structure
evonet

Evolutionary Networks
is.compatible

Check Compatibility of Splits
parafit

Test of host-parasite coevolution
drop.tip

Remove Tips in a Phylogenetic Tree
subtreeplot

Zoom on a Portion of a Phylogeny by Successive Clicks