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ape

This is the development version of ape.

To know more about ape: http://ape-package.ird.fr

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Version

Install

install.packages('ape')

Monthly Downloads

94,730

Version

5.6-2

License

GPL-2 | GPL-3

Maintainer

Emmanuel Paradis

Last Published

March 2nd, 2022

Functions in ape (5.6-2)

Moran's I Autocorrelation Index

Add a Scale Bar to a Phylogeny Plot

Manipulate DNA Sequences in Bit-Level Format

Recode Blocks of Indels

Amino Acid Sequences

all.equal.phylo

Global Comparison of two Phylogenies

Incomplete Distance Matrix Filling

Time-Dependent Birth-Death Models

Congruence among distance matrices

Print DNA or AA Sequence Alignement

Construction of Consensus Distance Matrix With SDM

branching.times

Branching Times of a Phylogenetic Tree

Ancestral Character Estimation

Phylogenetic Generalized Linear Mixed Model for Binary Data

Conversion Among Tree and Network Objects

as.phylo.formula

Conversion from Taxonomy Variables to Phylogenetic Trees

Phylogeny of the Families of Birds From Sibley and Ahlquist

Phylogeny of the Orders of Birds From Sibley and Ahlquist

Analyses of Phylogenetics and Evolution

Internal Ape Functions

Building Lists of Trees

Tree Estimation Based on an Improved Version of the NJ Algorithm

coalescent.intervals

Coalescent Intervals

Martins's (1997) Correlation Structure

collapse.singles

Collapse Single Nodes

Grafen's (1989) Correlation Structure

Vertex Degrees in Trees and Networks

Delete Alignment Gaps in DNA Sequences

Alignment Explorer With Multiple Devices

diversity.contrast.test

Diversity Contrast Test

collapsed.intervals

Collapsed Coalescent Intervals

all.equal.DNAbin

Compare DNA Sets

Plot of DNA Sequence Alignement

Axis on Side of Phylogeny

Lineages Through Time Plot

Test for Binary Tree

Balance of a Dichotomous Phylogenetic Tree

Estimation of Speciation and Extinction Rates With Birth-Death Models

compar.cheverud

Cheverud's Comparative Method

Pagel's ``lambda'' Correlation Structure

Correlations among Multiple Traits with Phylogenetic Signal

Molecular Dating With Mean Path Lengths

Molecular Dating With Penalized Likelihood

Manipulating Lists of Trees

Label Management

Branch Lengths Computation

Compute and Set Branching Times

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

Tree Bipartition and Bootstrapping Phylogenies

Theoretical Lineage-Through Time Plots

Minimum Variance Reduction

Base frequencies from DNA Sequences

Pairwise Distances from Genetic Data

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

Test of host-parasite coevolution

Blomberg et al.'s Correlation Structure

Initialize.corPhyl

Initialize a `corPhyl' Structure Object

Topological Distances Between Two Trees

Evolutionary Networks

Pairwise Distances from DNA Sequences

Tree Estimation Based on the Minimum Evolution Algorithm

Incomplete distances and edge weights of unrooted topology

Gamma-Statistic of Pybus and Harvey

Number of Cherries and Null Models of Trees

Check Compatibility of Splits

Leading and Trailing Alignment Gaps to N

Tools to Explore Files

is.monophyletic

Is Group Monophyletic

mcconwaysims.test

McConway-Sims Test of Homogeneous Diversification

Labelling the Nodes, Tips, and Edges of a Tree

Multiple regression through the origin

Check DNA Alignments

cophenetic.phylo

Pairwise Distances from a Phylogenetic Tree

Analysis of Diversification with Survival Models

Carnivora body sizes and life history traits

Concensus Trees

Tests of Constant Diversification Rates

Reversible Jump MCMC to Infer Demographic History

Remove Tips in a Phylogenetic Tree

Draw Additional Edges on a Plotted Tree

Principal Coordinate Analysis

Test if a Tree is Ultrametric

Depth and Heights of Nodes and Tips

Makes Node Labels

Random DNA Sequences

Neighbor-Joining Tree Estimation

Mantel Test for Similarity of Two Matrices

Plot Multiple Chronograms on the Same Scale

Continuous Character Simulation

Read DNA Sequences from GenBank via Internet

Find Paths of Nodes

Read Tree File in CAIC Format

Read DNA Sequences in a File

Tree Explorer With Multiple Devices

Conversion Among DNA Sequence Internal Formats

Define Similarity Matrix

Variance-Covariance Matrix to Tree

Checking Labels

checkValidPhylo

Check the Structure of a "phylo" Object

Zoom on a Portion of a Phylogeny

Split Frequencies and Conversion Among Split Classes

plot.phylo.extra

Extra Fuctions to Plot and Annotate Phylogenies

Tree Annotation

Tree Reconstruction from Incomplete Distances With NJ* or bio-NJ*

Fits a Bunch of Models with PhyML

Plot Tree With Time Axis

Compact Display of a Phylogeny

Root a Tree by Root-to-Tip Regression

Find Segregating Sites in DNA Sequences

Ornstein--Uhlenbeck Model for Continuous Characters

Plot Variance Components

Conversion Between Phylo and Matching Objects

Continuous Ancestral Character Estimation

Print Summary of a Phylogeny

Translation from DNA to Amino Acid Sequences

Read Tree File in Parenthetic Format

slowinskiguyer.test

Slowinski-Guyer Test of Homogeneous Diversification

Skyline Plot Estimate of Effective Population Size

solveAmbiguousBases

Solve Ambiguous Bases in DNA Sequences

Tree Reconstruction Based on the Triangles Method

Drawing Skyline Plot Graphs

Find Patterns in DNA Sequences

Brownian Correlation Structure

Compare Two "phylo" Objects

unique.multiPhylo

Revomes Duplicate Trees

Variance Components with Orthonormal Contrasts

Fits the Time-Dependent Yule Model

Fits the Yule Model With Covariates

Cytochrome b Gene Sequences of Woodmice

Write DNA Sequences in a File

Write Tree File in Parenthetic Format

Multiple Sequence Alignment with External Applications

Comparative Analysis with GEEs

Fits the Yule Model to a Phylogenetic Tree

write.nexus.data

Write Character Data in NEXUS Format

Lynch's Comparative Method

Identifies Edges of a Tree

Molecular Dating by Penalised Likelihood and Maximum Likelihood

Write Tree File in Nexus Format

Calculate Numbers of Phylogenetic Trees

Phylogenetic Correlation Structures

Five Independent Trees

Graphical Identification of Nodes and Tips

Matrix Exponential

NEXUS Data Example

correlogram.formula

Phylogenetic Correlogram

Probability Density Under Birth--Death Models

Mixed Font Labels for Plotting

Find Most Recent Common Ancestors Between Pairs

Definition of Vectors for Plotting or Annotating

Plot Phylogenies

plot.correlogram

Plot a Correlogram

Read Tree File in Nexus Format

read.nexus.data

Read Character Data In NEXUS Format

getAnnotationsGenBank

Read Annotations from GenBank

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

Phylogenetic Tree of 193 HIV-1 Sequences

Roots Phylogenetic Trees

Label Management

Zoom on a Portion of a Phylogeny by Successive Clicks

All subtrees of a Phylogenetic Tree

Ladderize a Tree

Minimum Spanning Tree

Collapse and Resolve Multichotomies

Multivariate Character Simulation

Phylogenetically Independent Contrasts

Discrete Character Simulation

Phylogenetically Independent Orthonormal Contrasts

Internal Reordering of Trees

richness.yule.test

Test of Diversification-Shift With the Yule Process

Swapping Sister Clades

Generate Random Trees

Species Tree Estimation

Generates Systematic Regular Trees

Phylogenetic Variance-covariance or Correlation Matrix

Compute Variance Component Estimates

Most Parsimonious Reconstruction