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ape (version 5.4-1)

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 DNA sequences, 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, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. 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

114,164

Version

5.4-1

License

GPL-2 | GPL-3

Maintainer

Emmanuel Paradis

Last Published

August 13th, 2020

Functions in ape (5.4-1)

ace

Ancestral Character Estimation
CADM.global

Congruence among distance matrices
DNAbin2indel

Recode Blocks of Indels
DNAbin

Manipulate DNA Sequences in Bit-Level Format
Initialize.corPhyl

Initialize a `corPhyl' Structure Object
Moran.I

Moran's I Autocorrelation Index
MPR

Most Parsimonious Reconstruction
AAbin

Amino Acid Sequences
LTT

Theoretical Lineage-Through Time Plots
alex

Alignment Explorer With Multiple Devices
bd.ext

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

Construction of Consensus Distance Matrix With SDM
add.scale.bar

Add a Scale Bar to a Phylogeny Plot
all.equal.DNAbin

Compare DNA Sets
base.freq

Base frequencies from DNA Sequences
all.equal.phylo

Global Comparison of two Phylogenies
apetools

Tools to Explore Files
birthdeath

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

Incomplete Distance Matrix Filling
boot.phylo

Tree Bipartition and Bootstrapping Phylogenies
balance

Balance of a Dichotomous Phylogenetic Tree
as.alignment

Conversion Among DNA Sequence Internal Formats
ape-package

Analyses of Phylogenetics and Evolution
ape-internal

Internal Ape Functions
as.bitsplits

Split Frequencies and Conversion Among Split Classes
cherry

Number of Cherries and Null Models of Trees
axisPhylo

Axis on Side of Phylogeny
bind.tree

Binds Trees
as.matching

Conversion Between Phylo and Matching Objects
BIONJ

Tree Estimation Based on an Improved Version of the NJ Algorithm
branching.times

Branching Times of a Phylogenetic Tree
bd.time

Time-Dependent Birth-Death Models
binaryPGLMM

Phylogenetic Generalized Linear Mixed Model for Binary Data
chronoMPL

Molecular Dating With Mean Path Lengths
compar.ou

Ornstein--Uhlenbeck Model for Continuous Characters
comparePhylo

Compare Two "phylo" Objects
c.phylo

Building Lists of Trees
bird.orders

Phylogeny of the Orders of Birds From Sibley and Ahlquist
coalescent.intervals

Coalescent Intervals
del.gaps

Delete Alignment Gaps in DNA Sequences
bird.families

Phylogeny of the Families of Birds From Sibley and Ahlquist
corphylo

Correlations among Multiple Traits with Phylogenetic Signal
corPagel

Pagel's ``lambda'' Correlation Structure
dnds

dN/dS Ratio
chronopl

Molecular Dating With Penalized Likelihood
corBrownian

Brownian Correlation Structure
kronoviz

Plot Multiple Chronograms on the Same Scale
delta.plot

Delta Plots
drop.tip

Remove Tips in a Phylogenetic Tree
consensus

Concensus Trees
label2table

Label Management
checkValidPhylo

Check the Structure of a "phylo" Object
checkLabel

Checking Labels
alview

Print DNA or AA Sequence Alignement
compar.gee

Comparative Analysis with GEEs
chiroptera

Bat Phylogeny
as.phylo

Conversion Among Tree and Network Objects
collapse.singles

Collapse Single Nodes
compar.lynch

Lynch's Comparative Method
as.phylo.formula

Conversion from Taxonomy Variables to Phylogenetic Trees
mrca

Find Most Recent Common Ancestors Between Pairs
makeNodeLabel

Makes Node Labels
makeLabel

Label Management
checkAlignment

Check DNA Alignments
diversi.time

Analysis of Diversification with Survival Models
chronos

Molecular Dating by Penalised Likelihood and Maximum Likelihood
edges

Draw Additional Edges on a Plotted Tree
cophenetic.phylo

Pairwise Distances from a Phylogenetic Tree
carnivora

Carnivora body sizes and life history traits
diversity.contrast.test

Diversity Contrast Test
clustal

Multiple Sequence Alignment with External Applications
compute.brlen

Branch Lengths Computation
compute.brtime

Compute and Set Branching Times
compar.cheverud

Cheverud's Comparative Method
correlogram.formula

Phylogenetic Correlogram
corGrafen

Grafen's (1989) Correlation Structure
corMartins

Martins's (1997) Correlation Structure
collapsed.intervals

Collapsed Coalescent Intervals
cophyloplot

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

Blomberg et al.'s Correlation Structure
dist.topo

Topological Distances Between Two Trees
mst

Minimum Spanning Tree
latag2n

Leading and Trailing Alignment Gaps to N
diversi.gof

Tests of Constant Diversification Rates
ladderize

Ladderize a Tree
evonet

Evolutionary Networks
plot.correlogram

Plot a Correlogram
pic.ortho

Phylogenetically Independent Orthonormal Contrasts
multi2di

Collapse and Resolve Multichotomies
is.monophyletic

Is Group Monophyletic
gammaStat

Gamma-Statistic of Pybus and Harvey
corClasses

Phylogenetic Correlation Structures
mat5M3ID

Five Trees
getAnnotationsGenBank

Read Annotations from GenBank
mat5Mrand

Five Independent Trees
rTraitMult

Multivariate Character Simulation
data.nex

NEXUS Data Example
lmorigin

Multiple regression through the origin
is.ultrametric

Test if a Tree is Ultrametric
dist.dna

Pairwise Distances from DNA Sequences
speciesTree

Species Tree Estimation
read.GenBank

Read DNA Sequences from GenBank via Internet
dist.gene

Pairwise Distances from Genetic Data
summary.phylo

Print Summary of a Phylogeny
stree

Generates Systematic Regular Trees
dbd

Probability Density Under Birth--Death Models
nodepath

Find Paths of Nodes
njs

Tree Reconstruction from Incomplete Distances With NJ* or bio-NJ*
ltt.plot

Lineages Through Time Plot
hivtree

Phylogenetic Tree of 193 HIV-1 Sequences
parafit

Test of host-parasite coevolution
trans

Translation from DNA to Amino Acid Sequences
def

Definition of Vectors for Plotting or Annotating
write.nexus.data

Write Character Data in NEXUS Format
multiphylo

Manipulating Lists of Trees
write.nexus

Write Tree File in Nexus Format
write.tree

Write Tree File in Parenthetic Format
yule

Fits the Yule Model to a Phylogenetic Tree
howmanytrees

Calculate Numbers of Phylogenetic Trees
ewLasso

Incomplete distances and edge weights of unrooted topology
FastME

Tree Estimation Based on the Minimum Evolution Algorithm
is.binary

Test for Binary Tree
is.compatible

Check Compatibility of Splits
node.depth

Depth and Heights of Nodes and Tips
nodelabels

Labelling the Nodes, Tips, and Edges of a Tree
identify.phylo

Graphical Identification of Nodes and Tips
node.dating

node.dating
print.phylo

Compact Display of a Phylogeny
read.gff

Read GFF Files
seg.sites

Find Segregating Sites in DNA Sequences
skyline

Skyline Plot Estimate of Effective Population Size
read.nexus

Read Tree File in Nexus Format
rDNAbin

Random DNA Sequences
mvr

Minimum Variance Reduction
mat3

Three Matrices
image.DNAbin

Plot of DNA Sequence Alignement
mantel.test

Mantel Test for Similarity of Two Matrices
mcconwaysims.test

McConway-Sims Test of Homogeneous Diversification
richness.yule.test

Test of Diversification-Shift With the Yule Process
matexpo

Matrix Exponential
rTraitCont

Continuous Character Simulation
rlineage

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

Roots Phylogenetic Trees
nj

Neighbor-Joining Tree Estimation
phydataplot

Tree Annotation
pcoa

Principal Coordinate Analysis
plot.phylo

Plot Phylogenies
mixedFontLabel

Mixed Font Labels for Plotting
mcmc.popsize

Reversible Jump MCMC to Infer Demographic History
phymltest

Fits a Bunch of Models with PhyML
plot.phylo.extra

Extra Fuctions to Plot and Annotate Phylogenies
read.nexus.data

Read Character Data In NEXUS Format
pic

Phylogenetically Independent Contrasts
trex

Tree Explorer With Multiple Devices
rTraitDisc

Discrete Character Simulation
treePop

Tree Popping
where

Find Patterns in DNA Sequences
updateLabel

Update Labels
plot.varcomp

Plot Variance Components
rotate

Swapping Sister Clades
plotTreeTime

Plot Tree With Time Axis
read.tree

Read Tree File in Parenthetic Format
which.edge

Identifies Edges of a Tree
varCompPhylip

Variance Components with Orthonormal Contrasts
read.caic

Read Tree File in CAIC Format
reconstruct

Continuous Ancestral Character Estimation
rtree

Generates Random Trees
rtt

Root a Tree by Root-to-Tip Regression
subtrees

All subtrees of a Phylogenetic Tree
zoom

Zoom on a Portion of a Phylogeny
reorder.phylo

Internal Reordering of Trees
read.dna

Read DNA Sequences in a File
slowinskiguyer.test

Slowinski-Guyer Test of Homogeneous Diversification
vcv

Phylogenetic Variance-covariance or Correlation Matrix
varcomp

Compute Variance Component Estimates
skylineplot

Drawing Skyline Plot Graphs
triangMtd

Tree Reconstruction Based on the Triangles Method
subtreeplot

Zoom on a Portion of a Phylogeny by Successive Clicks
vcv2phylo

Variance-Covariance Matrix to Tree
weight.taxo

Define Similarity Matrix
woodmouse

Cytochrome b Gene Sequences of Woodmice
unique.multiPhylo

Revomes Duplicate Trees
write.dna

Write DNA Sequences in a File
yule.time

Fits the Time-Dependent Yule Model
yule.cov

Fits the Yule Model With Covariates