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ape (version 3.0-10)

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, 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

3.0-10

License

GPL (>= 2)

Maintainer

Emmanuel Paradis

Last Published

September 10th, 2013

Functions in ape (3.0-10)

bird.orders

Phylogeny of the Orders of Birds From Sibley and Ahlquist
as.alignment

Conversion Among DNA Sequence Internal Formats
additive

Incomplete Distance Matrix Filling
all.equal.phylo

Global Comparison of two Phylogenies
BIONJ

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

Most Parsimonious Reconstruction
alex

Alignment Explorer With Multiple Devices
ape-internal

Internal Ape Functions
slowinskiguyer.test

Slowinski-Guyer Test of Homogeneous Diversification
bd.time

Time-Dependent Birth-Death Models
bd.ext

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

Coalescent Intervals
bind.tree

Binds Trees
branching.times

Branching Times of a Phylogenetic Tree
Initialize.corPhyl

Initialize a `corPhyl' Structure Object
balance

Balance of a Dichotomous Phylogenetic Tree
mrca

Find Most Recent Common Ancestors Between Pairs
birthdeath

Estimation of Speciation and Extinction Rates With Birth-Death Models
as.bitsplits

Conversion Among Split Classes
is.binary.tree

Test for Binary Tree
axisPhylo

Axis on Side of Phylogeny
Moran.I

Moran's I Autocorrelation Index
compar.cheverud

Cheverud's Comparative Method
is.monophyletic

Is Group Monophyletic
njs

Tree Reconstruction from Incomplete Distances With NJ* or bio-NJ*
c.phylo

Building Lists of Trees
chronos

Molecular Dating by Penalised Likelihood and Maximum Likelihood
mixedFontLabel

Mixed Font Labels for Plotting
chiroptera

Bat Phylogeny
read.nexus.data

Read Character Data In NEXUS Format
corPagel

Pagel's ``lambda'' Correlation Structure
yule

Fits the Yule Model to a Phylogenetic Tree
mantel.test

Mantel Test for Similarity of Two Matrices
mat3

Three Matrices
kronoviz

Plot Multiple Chronograms on the Same Scale
chronoMPL

Molecular Dating With Mean Path Lengths
edges

Draw Additional Edges on a Plotted Tree
mat5Mrand

Five Independent Trees
write.tree

Write Tree File in Parenthetic Format
FastME

Tree Estimation Based on the Minimum Evolution Algorithm
matexpo

Matrix Exponential
ladderize

Ladderize a Tree
is.ultrametric

Test if a Tree is Ultrametric
bird.families

Phylogeny of the Families of Birds From Sibley and Ahlquist
summary.phylo

Print Summary of a Phylogeny
skyline

Skyline Plot Estimate of Effective Population Size
pcoa

Principal Coordinate Analysis
as.phylo.formula

Conversion from Taxonomy Variables to Phylogenetic Trees
landplants

Gene Tree of 36 Landplant rbcL Sequences
read.nexus

Read Tree File in Nexus Format
collapse.singles

Collapse Single Nodes
clustal

Multiple Sequence Alignment with External Applications
evonet

Evolutionary Networks
plot.varcomp

Plot Variance Components
corMartins

Martins's (1997) Correlation Structure
rtree

Generates Random Trees
richness.yule.test

Test of Diversification-Shift With the Yule Process
rTraitCont

Continuous Character Simulation
read.GenBank

Read DNA Sequences from GenBank via Internet
is.compatible

Check Compatibility of Splits
seg.sites

Find Segregating Sites in DNA Sequences
unique.multiPhylo

Revomes Duplicate Trees
write.nexus.data

Write Character Data in NEXUS Format
where

Find Patterns in DNA Sequences
yule.time

Fits the Time-Dependent Yule Model
ewLasso

Incomplete distances and edge weights of unrooted topology
rTraitMult

Multivariate Character Simulation
corBrownian

Brownian Correlation Structure
triangMtd

Tree Reconstruction Based on the Triangles Method
mcconwaysims.test

McConway-Sims Test of Homogeneous Diversification
as.matching

Conversion Between Phylo and Matching Objects
multiphylo

Manipulating Lists of Trees
which.edge

Identifies Edges of a Tree
print.phylo

Compact Display of a Phylogeny
write.nexus

Write Tree File in Nexus Format
woodmouse

Cytochrome b Gene Sequences of Woodmice
as.phylo

Conversion Among Tree and Network Objects
node.depth

Depth and Heights of Nodes and Tips
pic.ortho

Phylogenetically Independent Orthonormal Contrasts
mcmc.popsize

Reversible Jump MCMC to Infer Demographic History
boot.phylo

Tree Bipartition and Bootstrapping Phylogenies
subtrees

All subtrees of a Phylogenetic Tree
corGrafen

Grafen's (1989) Correlation Structure
add.scale.bar

Add a Scale Bar to a Phylogeny Plot
ltt.plot

Lineages Through Time Plot
cherry

Number of Cherries and Null Models of Trees
cophenetic.phylo

Pairwise Distances from a Phylogenetic Tree
hivtree

Phylogenetic Tree of 193 HIV-1 Sequences
base.freq

Base frequencies from DNA Sequences
ape-package

Analyses of Phylogenetics and Evolution
howmanytrees

Calculate Numbers of Phylogenetic Trees
read.caic

Read Tree File in CAIC Format
identify.phylo

Graphical Identification of Nodes and Tips
treePop

Tree Popping
root

Roots Phylogenetic Trees
rlineage

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

Tree Explorer With Multiple Devices
skylineplot

Drawing Skyline Plot Graphs
SDM

Construction of Consensus Distance Matrix With SDM
weight.taxo

Define Similarity Matrix
speciesTree

Species Tree Estimation
makeNodeLabel

Makes Node Labels
zoom

Zoom on a Portion of a Phylogeny
chronopl

Molecular Dating With Penalized Likelihood
makeLabel

Label Management
image.DNAbin

Plot of DNA Sequence Alignement
carnivora

Carnivora body sizes and life history traits
compar.lynch

Lynch's Comparative Method
nj

Neighbor-Joining Tree Estimation
gammaStat

Gamma-Statistic of Pybus and Harvey
consensus

Concensus Trees
mvr

Minimum Variance Reduction
pic

Phylogenetically Independent Contrasts
corClasses

Phylogenetic Correlation Structures
DNAbin

Manipulate DNA Sequences in Bit-Level Format
stree

Generates Systematic Regular Trees
subtreeplot

Zoom on a Portion of a Phylogeny by Successive Clicks
lmorigin

Multiple regression through the origin
write.dna

Write DNA Sequences in a File
read.dna

Read DNA Sequences in a File
read.tree

Read Tree File in Parenthetic Format
nodelabels

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

Gene Tree of 32 opsin Sequences
diversi.gof

Tests of Constant Diversification Rates
multi2di

Collapse and Resolve Multichotomies
mst

Minimum Spanning Tree
vcv

Phylogenetic Variance-covariance or Correlation Matrix
collapsed.intervals

Collapsed Coalescent Intervals
rotate

Swapping Sister Clades
del.gaps

Delete Alignment Gaps in DNA Sequences
varcomp

Compute Variance Component Estimates
ace

Ancestral Character Estimation
compar.gee

Comparative Analysis with GEEs
CADM.global

Congruence among distance matrices
reorder.phylo

Internal Reordering of Trees
varCompPhylip

Variance Components with Orthonormal Contrasts
dist.dna

Pairwise Distances from DNA Sequences
phymltest

Fits a Bunch of Models with PhyML
plot.phylo

Plot Phylogenies
mat5M3ID

Five Trees
plot.correlogram

Plot a Correlogram
yule.cov

Fits the Yule Model With Covariates
rTraitDisc

Discrete Character Simulation
parafit

Test of host-parasite coevolution
correlogram.formula

Phylogenetic Correlogram
dist.gene

Pairwise Distances from Genetic Data
delta.plot

Delta Plots
cophyloplot

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

Analysis of Diversification with Survival Models
corBlomberg

Blomberg et al.'s Correlation Structure
dist.topo

Topological Distances Between Two Trees
data.nex

NEXUS Data Example
dbd

Probability Density Under Birth--Death Models
compute.brtime

Compute and Set Branching Times
compar.ou

Ornstein--Uhlenbeck Model for Continuous Characters
compute.brlen

Branch Lengths Computation
diversity.contrast.test

Diversity Contrast Test
drop.tip

Remove Tips in a Phylogenetic Tree