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ape (version 2.5-1)

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

2.5-1

License

GPL (>= 2)

Maintainer

Emmanuel Paradis

Last Published

April 6th, 2010

Functions in ape (2.5-1)

as.phylo

Conversion Among Tree Objects
DNAbin

Manipulate DNA Sequences in Bit-Level Format
cophenetic.phylo

Pairwise Distances from a Phylogenetic Tree
ape-defunct

Defunct Ape Functions
data.nex

NEXUS Data Example
NPRS.criterion

Objective Function Employed in Nonparametric Rate Smoothing
ladderize

Ladderize a Tree
cophyloplot

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

Initialize a `corPhyl' Structure Object
all.equal.phylo

Global Comparison of two Phylogenies
read.caic

Read Tree File in CAIC Format
delta.plot

Delta Plots
compar.cheverud

Cheverud's Comparative Method
boot.phylo

Tree Bipartition and Bootstrapping Phylogenies
bird.families

Phylogeny of the Families of Birds From Sibley and Ahlquist
makeNodeLabel

Makes Node Labels
diversi.gof

Tests of Constant Diversification Rates
reorder.phylo

Internal Reordering of Trees
ape-internal

Internal Ape Functions
read.tree

Read Tree File in Parenthetic Format
woodmouse

Cytochrome b Gene Sequences of Woodmice
rTraitCont

Continuous Character Simulation
chronopl

Molecular Dating With Penalized Likelihood
diversi.time

Analysis of Diversification with Survival Models
corBlomberg

Blomberg et al.'s Correlation Structure
CADM.global

Congruence among distance matrices
Moran.I

Moran's I Autocorrelation Index
bd.ext

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

Neighbor-Joining Tree Estimation
corClasses

Phylogenetic Correlation Structures
phymltest

Fits a Bunch of Models with PhyML
dist.topo

Topological Distances Between Two Trees
coalescent.intervals

Coalescent Intervals
opsin

Gene Tree of 32 opsin Sequences
hivtree

Phylogenetic Tree of 193 HIV-1 Sequences
axisPhylo

Axis on Side of Phylogeny
BIONJ

Tree Estimation Based on an Improved Version of the NJ Algorithm
identify.phylo

Graphical Identification of Nodes and Tips
birthdeath

Estimation of Speciation and Extinction Rates With Birth-Death Models
evolve.phylo

Ancestral Character Simulation
correlogram.formula

Phylogenetic Correlogram
read.GenBank

Read DNA Sequences from GenBank via Internet
branching.times

Branching Times of a Phylogenetic Tree
ace

Ancestral Character Estimation
del.gaps

Delete Alignment Gaps in DNA Sequences
chronoMPL

Molecular Dating With Mean Path Lengths
mcmc.popsize

Reversible Jump MCMC to Infer Demographic History
bird.orders

Phylogeny of the Orders of Birds From Sibley and Ahlquist
cherry

Number of Cherries and Null Models of Trees
print.phylo

Compact Display of a Phylogeny
collapsed.intervals

Collapsed Coalescent Intervals
root

Roots Phylogenetic Trees
balance

Balance of a Dichotomous Phylogenetic Tree
plot.ancestral

Plot Ancestral Character Values on a Tree
stree

Generates Systematic Regular Trees
is.binary.tree

Test for Binary Tree
compar.gee

Comparative Analysis with GEEs
lmorigin

Multiple regression through the origin
base.freq

Base frequencies from DNA Sequences
which.edge

Identifies Edges of a Tree
mantel.test

Mantel Test for Similarity of Two Matrices
chiroptera

Bat Phylogeny
makeLabel

Label Management
howmanytrees

Calculate Numbers of Phylogenetic Trees
FastME

Tree Estimation Based on the Minimum Evolution Algorithm
plot.varcomp

Plot Variance Components
parafit

Test of host-parasite coevolution
unique.multiPhylo

Revomes Duplicate Trees
varcomp

Compute Variance Component Estimates
is.ultrametric

Test if a Tree is Ultrametric
pcoa

Principal Coordinate Analysis
yule.cov

Fits the Yule Model With Covariates
nodelabels

Labelling the Nodes, Tips, and Edges of a Tree
mat5M3ID

Five Trees
chronogram

Chronogram Computed by Nonparametric Rate Smoothing
corBrownian

Brownian Correlation Structure
collapse.singles

Collapse Single Nodes
matexpo

Matrix Exponential
subtrees

All subtrees of a Phylogenetic Tree
skylineplot

Drawing Skyline Plot Graphs
as.matching

Conversion Between Phylo and Matching Objects
dist.dna

Pairwise Distances from DNA Sequences
plot.phylo

Plot Phylogenies
subtreeplot

Zoom on a Portion of a Phylogeny by Successive Clicks
landplants

Gene Tree of 36 Landplant rbcL Sequences
yule.time

Fits the Time-Dependent Yule Model
as.phylo.formula

Conversion from Taxonomy Variables to Phylogenetic Trees
carnivora

Carnivora body sizes and life history traits
zoom

Zoom on a Portion of a Phylogeny
read.nexus.data

Read Character Data In NEXUS Format
rtree

Generates Random Trees
plot.correlogram

Plot a Correlogram
corGrafen

Grafen's (1989) Correlation Structure
write.nexus.data

Write Character Data In NEXUS Format
add.scale.bar

Add a Scale Bar to a Phylogeny Plot
node.depth

Depth of Nodes and Tips
ltt.plot

Lineages Through Time Plot
consensus

Concensus Trees
bind.tree

Binds Trees
ape-package

Analyses of Phylogenetics and Evolution
seg.sites

Find Segregating Sites in DNA Sequences
rotate

Swapping sister clades
edges

Draw Additional Edges on a Plotted Tree
compar.lynch

Lynch's Comparative Method
mst

Minimum Spanning Tree
yule

Fits Yule Model to a Phylogenetic Tree
summary.phylo

Print Summary of a Phylogeny
corPagel

Pagel's ``lambda'' Correlation Structure
read.dna

Read DNA Sequences in a File
write.tree

Write Tree File in Parenthetic Format
mrca

Find Most Recent Common Ancestors Between Pairs
compute.brlen

Branch Lengths Computation
read.nexus

Read Tree File in Nexus Format
write.dna

Write DNA Sequences in a File
drop.tip

Remove Tips in a Phylogenetic Tree
gammaStat

Gamma-Statistic of Pybus and Harvey
skyline

Skyline Plot Estimate of Effective Population Size
is.monophyletic

Is Group Monophyletic
mat5Mrand

Five Independent Trees
ratogram

Ratogram Computed by Nonparametric Rate Smoothing
pic

Phylogenetically Independent Contrasts
rTraitDisc

Discrete Character Simulation
as.alignment

Conversion Among DNA Sequence Internal Formats
vcv.phylo

Phylogenetic Variance-covariance or Correlation Matrix
GC.content

Content in GC from DNA Sequences
compar.ou

Ornstein--Uhlenbeck Model for Continuous Characters
corMartins

Martins's (1997) Correlation Structure
dist.gene

Pairwise Distances from Genetic Data
mat3

Three Matrices
multi2di

Collapse and Resolve Multichotomies
weight.taxo

Define Similarity Matrix
write.nexus

Write Tree File in Nexus Format
multiphylo

Manipulating Lists of Trees
c.phylo

Building Lists of Trees
mixedFontLabel

Mixed Font Labels for Plotting