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ape (version 3.4)

Analyses of Phylogenetics and Evolution

Description

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

87,302

Version

3.4

License

GPL (>= 2)

Maintainer

Emmanuel Paradis

Last Published

November 29th, 2015

Functions in ape (3.4)

as.alignment

Conversion Among DNA Sequence Internal Formats
additive

Incomplete Distance Matrix Filling
balance

Balance of a Dichotomous Phylogenetic Tree
as.phylo

Conversion Among Tree and Network Objects
chronoMPL

Molecular Dating With Mean Path Lengths
binaryPGLMM

Phylogenetic Generalized Linear Mixed Model for Binary Data
alview

Print DNA Sequence Alignements
is.ultrametric

Test if a Tree is Ultrametric
checkValidPhylo

Check the Structure of a "phylo" Object
DNAbin2indel

Recode Blocks of Indels
chiroptera

Bat Phylogeny
chronopl

Molecular Dating With Penalized Likelihood
as.phylo.formula

Conversion from Taxonomy Variables to Phylogenetic Trees
compar.gee

Comparative Analysis with GEEs
Moran.I

Moran's I Autocorrelation Index
edges

Draw Additional Edges on a Plotted Tree
dbd

Probability Density Under Birth--Death Models
makeNodeLabel

Makes Node Labels
corphylo

Correlations among Multiple Traits with Phylogenetic Signal
carnivora

Carnivora body sizes and life history traits
as.matching

Conversion Between Phylo and Matching Objects
bind.tree

Binds Trees
compar.lynch

Lynch's Comparative Method
alex

Alignment Explorer With Multiple Devices
compar.ou

Ornstein--Uhlenbeck Model for Continuous Characters
slowinskiguyer.test

Slowinski-Guyer Test of Homogeneous Diversification
nodelabels

Labelling the Nodes, Tips, and Edges of a Tree
coalescent.intervals

Coalescent Intervals
axisPhylo

Axis on Side of Phylogeny
reorder.phylo

Internal Reordering of Trees
del.gaps

Delete Alignment Gaps in DNA Sequences
chronos

Molecular Dating by Penalised Likelihood and Maximum Likelihood
bd.time

Time-Dependent Birth-Death Models
corMartins

Martins's (1997) Correlation Structure
compute.brlen

Branch Lengths Computation
collapse.singles

Collapse Single Nodes
kronoviz

Plot Multiple Chronograms on the Same Scale
dist.dna

Pairwise Distances from DNA Sequences
diversi.time

Analysis of Diversification with Survival Models
ladderize

Ladderize a Tree
clustal

Multiple Sequence Alignment with External Applications
consensus

Concensus Trees
all.equal.phylo

Global Comparison of two Phylogenies
ace

Ancestral Character Estimation
node.depth

Depth and Heights of Nodes and Tips
BIONJ

Tree Estimation Based on an Improved Version of the NJ Algorithm
as.bitsplits

Split Frequencies and Conversion Among Split Classes
read.caic

Read Tree File in CAIC Format
varCompPhylip

Variance Components with Orthonormal Contrasts
bird.orders

Phylogeny of the Orders of Birds From Sibley and Ahlquist
multi2di

Collapse and Resolve Multichotomies
ewLasso

Incomplete distances and edge weights of unrooted topology
SDM

Construction of Consensus Distance Matrix With SDM
boot.phylo

Tree Bipartition and Bootstrapping Phylogenies
collapsed.intervals

Collapsed Coalescent Intervals
corBrownian

Brownian Correlation Structure
identify.phylo

Graphical Identification of Nodes and Tips
data.nex

NEXUS Data Example
trex

Tree Explorer With Multiple Devices
read.nexus

Read Tree File in Nexus Format
gammaStat

Gamma-Statistic of Pybus and Harvey
corGrafen

Grafen's (1989) Correlation Structure
drop.tip

Remove Tips in a Phylogenetic Tree
rTraitCont

Continuous Character Simulation
read.GenBank

Read DNA Sequences from GenBank via Internet
opsin

Gene Tree of 32 opsin Sequences
corBlomberg

Blomberg et al.'s Correlation Structure
seg.sites

Find Segregating Sites in DNA Sequences
label2table

Label Management
howmanytrees

Calculate Numbers of Phylogenetic Trees
is.binary.tree

Test for Binary Tree
bird.families

Phylogeny of the Families of Birds From Sibley and Ahlquist
branching.times

Branching Times of a Phylogenetic Tree
bd.ext

Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
Initialize.corPhyl

Initialize a `corPhyl' Structure Object
plot.correlogram

Plot a Correlogram
matexpo

Matrix Exponential
c.phylo

Building Lists of Trees
CADM.global

Congruence among distance matrices
dist.gene

Pairwise Distances from Genetic Data
birthdeath

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

Plots two phylogenetic trees face to face with links between the tips.
ape-internal

Internal Ape Functions
mat3

Three Matrices
mcmc.popsize

Reversible Jump MCMC to Infer Demographic History
skyline

Skyline Plot Estimate of Effective Population Size
rtree

Generates Random Trees
richness.yule.test

Test of Diversification-Shift With the Yule Process
print.phylo

Compact Display of a Phylogeny
write.dna

Write DNA Sequences in a File
mrca

Find Most Recent Common Ancestors Between Pairs
corClasses

Phylogenetic Correlation Structures
mst

Minimum Spanning Tree
which.edge

Identifies Edges of a Tree
zoom

Zoom on a Portion of a Phylogeny
skylineplot

Drawing Skyline Plot Graphs
ltt.plot

Lineages Through Time Plot
subtrees

All subtrees of a Phylogenetic Tree
unique.multiPhylo

Revomes Duplicate Trees
triangMtd

Tree Reconstruction Based on the Triangles Method
speciesTree

Species Tree Estimation
cophenetic.phylo

Pairwise Distances from a Phylogenetic Tree
diversi.gof

Tests of Constant Diversification Rates
summary.phylo

Print Summary of a Phylogeny
mvr

Minimum Variance Reduction
multiphylo

Manipulating Lists of Trees
vcv2phylo

Variance-Covariance Matrix to Tree
subtreeplot

Zoom on a Portion of a Phylogeny by Successive Clicks
is.monophyletic

Is Group Monophyletic
yule.time

Fits the Time-Dependent Yule Model
read.dna

Read DNA Sequences in a File
where

Find Patterns in DNA Sequences
write.tree

Write Tree File in Parenthetic Format
nodepath

Find Paths of Nodes
write.nexus.data

Write Character Data in NEXUS Format
delta.plot

Delta Plots
cherry

Number of Cherries and Null Models of Trees
is.compatible

Check Compatibility of Splits
pic

Phylogenetically Independent Contrasts
treePop

Tree Popping
base.freq

Base frequencies from DNA Sequences
rTraitMult

Multivariate Character Simulation
mcconwaysims.test

McConway-Sims Test of Homogeneous Diversification
phymltest

Fits a Bunch of Models with PhyML
corPagel

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

Write Tree File in Nexus Format
ape-package

Analyses of Phylogenetics and Evolution
mat5Mrand

Five Independent Trees
MPR

Most Parsimonious Reconstruction
plot.phylo

Plot Phylogenies
read.tree

Read Tree File in Parenthetic Format
diversity.contrast.test

Diversity Contrast Test
evonet

Evolutionary Networks
mantel.test

Mantel Test for Similarity of Two Matrices
makeLabel

Label Management
image.DNAbin

Plot of DNA Sequence Alignement
plot.varcomp

Plot Variance Components
lmorigin

Multiple regression through the origin
rTraitDisc

Discrete Character Simulation
read.nexus.data

Read Character Data In NEXUS Format
reconstruct

Continuous Ancestral Character Estimation
stree

Generates Systematic Regular Trees
yule.cov

Fits the Yule Model With Covariates
rtt

Root a Tree by Root-to-Tip Regression
woodmouse

Cytochrome b Gene Sequences of Woodmice
nj

Neighbor-Joining Tree Estimation
compute.brtime

Compute and Set Branching Times
vcv

Phylogenetic Variance-covariance or Correlation Matrix
phydataplot

Tree Annotation
varcomp

Compute Variance Component Estimates
rotate

Swapping Sister Clades
DNAbin

Manipulate DNA Sequences in Bit-Level Format
add.scale.bar

Add a Scale Bar to a Phylogeny Plot
def

Definition of Vectors for Plotting or Annotating
FastME

Tree Estimation Based on the Minimum Evolution Algorithm
mat5M3ID

Five Trees
mixedFontLabel

Mixed Font Labels for Plotting
compar.cheverud

Cheverud's Comparative Method
pcoa

Principal Coordinate Analysis
pic.ortho

Phylogenetically Independent Orthonormal Contrasts
parafit

Test of host-parasite coevolution
njs

Tree Reconstruction from Incomplete Distances With NJ* or bio-NJ*
correlogram.formula

Phylogenetic Correlogram
rlineage

Tree Simulation Under the Time-Dependent Birth--Death Models
weight.taxo

Define Similarity Matrix
yule

Fits the Yule Model to a Phylogenetic Tree
hivtree

Phylogenetic Tree of 193 HIV-1 Sequences
LTT

Theoretical Lineage-Through Time Plots
dist.topo

Topological Distances Between Two Trees
root

Roots Phylogenetic Trees
landplants

Gene Tree of 36 Landplant rbcL Sequences