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ape (version 2.5-3)

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

87,302

Version

2.5-3

License

GPL (>= 2)

Maintainer

Emmanuel Paradis

Last Published

June 15th, 2010

Functions in ape (2.5-3)

Initialize.corPhyl

Initialize a `corPhyl' Structure Object
ape-internal

Internal Ape Functions
bird.orders

Phylogeny of the Orders of Birds From Sibley and Ahlquist
cherry

Number of Cherries and Null Models of Trees
ape-defunct

Defunct Ape Functions
c.phylo

Building Lists of Trees
bind.tree

Binds Trees
Moran.I

Moran's I Autocorrelation Index
bird.families

Phylogeny of the Families of Birds From Sibley and Ahlquist
as.phylo.formula

Conversion from Taxonomy Variables to Phylogenetic Trees
cophenetic.phylo

Pairwise Distances from a Phylogenetic Tree
balance

Balance of a Dichotomous Phylogenetic Tree
chiroptera

Bat Phylogeny
compute.brlen

Branch Lengths Computation
bd.ext

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

Matrix Exponential
data.nex

NEXUS Data Example
GC.content

Content in GC from DNA Sequences
corGrafen

Grafen's (1989) Correlation Structure
as.alignment

Conversion Among DNA Sequence Internal Formats
corBrownian

Brownian Correlation Structure
add.scale.bar

Add a Scale Bar to a Phylogeny Plot
cophyloplot

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

Axis on Side of Phylogeny
opsin

Gene Tree of 32 opsin Sequences
coalescent.intervals

Coalescent Intervals
del.gaps

Delete Alignment Gaps in DNA Sequences
consensus

Concensus Trees
birthdeath

Estimation of Speciation and Extinction Rates With Birth-Death Models
compar.ou

Ornstein--Uhlenbeck Model for Continuous Characters
dist.dna

Pairwise Distances from DNA Sequences
as.phylo

Conversion Among Tree Objects
chronoMPL

Molecular Dating With Mean Path Lengths
branching.times

Branching Times of a Phylogenetic Tree
collapse.singles

Collapse Single Nodes
compar.cheverud

Cheverud's Comparative Method
corClasses

Phylogenetic Correlation Structures
carnivora

Carnivora body sizes and life history traits
mantel.test

Mantel Test for Similarity of Two Matrices
corBlomberg

Blomberg et al.'s Correlation Structure
all.equal.phylo

Global Comparison of two Phylogenies
corPagel

Pagel's ``lambda'' Correlation Structure
base.freq

Base frequencies from DNA Sequences
ape-package

Analyses of Phylogenetics and Evolution
correlogram.formula

Phylogenetic Correlogram
ace

Ancestral Character Estimation
corMartins

Martins's (1997) Correlation Structure
dist.gene

Pairwise Distances from Genetic Data
gammaStat

Gamma-Statistic of Pybus and Harvey
compar.gee

Comparative Analysis with GEEs
hivtree

Phylogenetic Tree of 193 HIV-1 Sequences
chronopl

Molecular Dating With Penalized Likelihood
compar.lynch

Lynch's Comparative Method
delta.plot

Delta Plots
BIONJ

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

Analysis of Diversification with Survival Models
collapsed.intervals

Collapsed Coalescent Intervals
reorder.phylo

Internal Reordering of Trees
rtree

Generates Random Trees
as.matching

Conversion Between Phylo and Matching Objects
DNAbin

Manipulate DNA Sequences in Bit-Level Format
yule.time

Fits the Time-Dependent Yule Model
subtreeplot

Zoom on a Portion of a Phylogeny by Successive Clicks
pic

Phylogenetically Independent Contrasts
read.caic

Read Tree File in CAIC Format
unique.multiPhylo

Revomes Duplicate Trees
plot.varcomp

Plot Variance Components
skylineplot

Drawing Skyline Plot Graphs
zoom

Zoom on a Portion of a Phylogeny
yule

Fits Yule Model to a Phylogenetic Tree
read.dna

Read DNA Sequences in a File
read.nexus.data

Read Character Data In NEXUS Format
phymltest

Fits a Bunch of Models with PhyML
boot.phylo

Tree Bipartition and Bootstrapping Phylogenies
parafit

Test of host-parasite coevolution
plot.phylo

Plot Phylogenies
mrca

Find Most Recent Common Ancestors Between Pairs
CADM.global

Congruence among distance matrices
mixedFontLabel

Mixed Font Labels for Plotting
identify.phylo

Graphical Identification of Nodes and Tips
is.ultrametric

Test if a Tree is Ultrametric
is.binary.tree

Test for Binary Tree
is.monophyletic

Is Group Monophyletic
howmanytrees

Calculate Numbers of Phylogenetic Trees
diversi.gof

Tests of Constant Diversification Rates
landplants

Gene Tree of 36 Landplant rbcL Sequences
makeLabel

Label Management
edges

Draw Additional Edges on a Plotted Tree
makeNodeLabel

Makes Node Labels
dist.topo

Topological Distances Between Two Trees
mcmc.popsize

Reversible Jump MCMC to Infer Demographic History
drop.tip

Remove Tips in a Phylogenetic Tree
node.depth

Depth of Nodes and Tips
nj

Neighbor-Joining Tree Estimation
mst

Minimum Spanning Tree
multiphylo

Manipulating Lists of Trees
ladderize

Ladderize a Tree
mat5Mrand

Five Independent Trees
FastME

Tree Estimation Based on the Minimum Evolution Algorithm
nodelabels

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

Multiple regression through the origin
pcoa

Principal Coordinate Analysis
rTraitCont

Continuous Character Simulation
stree

Generates Systematic Regular Trees
subtrees

All subtrees of a Phylogenetic Tree
woodmouse

Cytochrome b Gene Sequences of Woodmice
write.tree

Write Tree File in Parenthetic Format
vcv.phylo

Phylogenetic Variance-covariance or Correlation Matrix
read.tree

Read Tree File in Parenthetic Format
yule.cov

Fits the Yule Model With Covariates
read.GenBank

Read DNA Sequences from GenBank via Internet
rTraitDisc

Discrete Character Simulation
which.edge

Identifies Edges of a Tree
write.dna

Write DNA Sequences in a File
multi2di

Collapse and Resolve Multichotomies
varcomp

Compute Variance Component Estimates
mat3

Three Matrices
read.nexus

Read Tree File in Nexus Format
mat5M3ID

Five Trees
ltt.plot

Lineages Through Time Plot
print.phylo

Compact Display of a Phylogeny
plot.correlogram

Plot a Correlogram
seg.sites

Find Segregating Sites in DNA Sequences
write.nexus.data

Write Character Data In NEXUS Format
weight.taxo

Define Similarity Matrix
summary.phylo

Print Summary of a Phylogeny
root

Roots Phylogenetic Trees
write.nexus

Write Tree File in Nexus Format
skyline

Skyline Plot Estimate of Effective Population Size
rotate

Swapping sister clades