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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

87,302

Version

5.7

License

GPL-2 | GPL-3

Maintainer

Emmanuel Paradis

Last Published

February 16th, 2023

Functions in ape (5.7)

Recode Blocks of Indels

Manipulate DNA Sequences in Bit-Level Format

Most Parsimonious Reconstruction

Amino Acid Sequences

Moran's I Autocorrelation Index

Congruence among distance matrices

Construction of Consensus Distance Matrix With SDM

Ancestral Character Estimation

all.equal.phylo

Global Comparison of two Phylogenies

Print DNA or AA Sequence Alignement

Theoretical Lineage-Through Time Plots

Initialize.corPhyl

Initialize a `corPhyl' Structure Object

Add a Scale Bar to a Phylogeny Plot

Incomplete Distance Matrix Filling

Conversion Among DNA Sequence Internal Formats

Analyses of Phylogenetics and Evolution

Internal Ape Functions

Tools to Explore Files

Alignment Explorer With Multiple Devices

Split Frequencies and Conversion Among Split Classes

Conversion Among Tree and Network Objects

Time-Dependent Birth-Death Models

all.equal.DNAbin

Compare DNA Sets

Axis on Side of Phylogeny

as.phylo.formula

Conversion from Taxonomy Variables to Phylogenetic Trees

Conversion Between Phylo and Matching Objects

Phylogenetic Generalized Linear Mixed Model for Binary Data

Balance of a Dichotomous Phylogenetic Tree

Base frequencies from DNA Sequences

Check DNA Alignments

Carnivora body sizes and life history traits

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

Phylogeny of the Orders of Birds From Sibley and Ahlquist

Estimation of Speciation and Extinction Rates With Birth-Death Models

Phylogeny of the Families of Birds From Sibley and Ahlquist

Tree Bipartition and Bootstrapping Phylogenies

Tree Estimation Based on an Improved Version of the NJ Algorithm

branching.times

Branching Times of a Phylogenetic Tree

Molecular Dating by Penalised Likelihood and Maximum Likelihood

checkValidPhylo

Check the Structure of a "phylo" Object

Molecular Dating With Penalized Likelihood

Number of Cherries and Null Models of Trees

Building Lists of Trees

Molecular Dating With Mean Path Lengths

coalescent.intervals

Coalescent Intervals

Checking Labels

Multiple Sequence Alignment with External Applications

collapse.singles

Collapse Single Nodes

Lynch's Comparative Method

Branch Lengths Computation

Compute and Set Branching Times

Comparative Analysis with GEEs

cophenetic.phylo

Pairwise Distances from a Phylogenetic Tree

Compare Two "phylo" Objects

Ornstein--Uhlenbeck Model for Continuous Characters

collapsed.intervals

Collapsed Coalescent Intervals

compar.cheverud

Cheverud's Comparative Method

Concensus Trees

Grafen's (1989) Correlation Structure

Phylogenetic Correlation Structures

NEXUS Data Example

Correlations among Multiple Traits with Phylogenetic Signal

Pagel's ``lambda'' Correlation Structure

correlogram.formula

Phylogenetic Correlogram

Brownian Correlation Structure

Blomberg et al.'s Correlation Structure

Martins's (1997) Correlation Structure

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

Topological Distances Between Two Trees

Definition of Vectors for Plotting or Annotating

Analysis of Diversification with Survival Models

Pairwise Distances from Genetic Data

Delete Alignment Gaps in DNA Sequences

Vertex Degrees in Trees and Networks

Probability Density Under Birth--Death Models

Tests of Constant Diversification Rates

Pairwise Distances from DNA Sequences

getAnnotationsGenBank

Read Annotations from GenBank

diversity.contrast.test

Diversity Contrast Test

Incomplete distances and edge weights of unrooted topology

Gamma-Statistic of Pybus and Harvey

Remove Tips in a Phylogenetic Tree

Evolutionary Networks

Tree Estimation Based on the Minimum Evolution Algorithm

Draw Additional Edges on a Plotted Tree

Phylogenetic Tree of 193 HIV-1 Sequences

Plot of DNA Sequence Alignement

Check Compatibility of Splits

is.monophyletic

Is Group Monophyletic

Test if a Tree is Ultrametric

Test for Binary Tree

Graphical Identification of Nodes and Tips

Label Management

Ladderize a Tree

Plot Multiple Chronograms on the Same Scale

Calculate Numbers of Phylogenetic Trees

Makes Node Labels

Five Independent Trees

Leading and Trailing Alignment Gaps to N

Mantel Test for Similarity of Two Matrices

Matrix Exponential

Lineages Through Time Plot

Label Management

Multiple regression through the origin

Minimum Spanning Tree

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

Find Most Recent Common Ancestors Between Pairs

mcconwaysims.test

McConway-Sims Test of Homogeneous Diversification

Mixed Font Labels for Plotting

Collapse and Resolve Multichotomies

Reversible Jump MCMC to Infer Demographic History

Manipulating Lists of Trees

Neighbor-Joining Tree Estimation

Minimum Variance Reduction

Labelling the Nodes, Tips, and Edges of a Tree

Principal Coordinate Analysis

Phylogenetically Independent Orthonormal Contrasts

Depth and Heights of Nodes and Tips

Test of host-parasite coevolution

Phylogenetically Independent Contrasts

Find Paths of Nodes

Fits a Bunch of Models with PhyML

Tree Annotation

Random DNA Sequences

plot.correlogram

Plot a Correlogram

Continuous Character Simulation

Plot Tree With Time Axis

Discrete Character Simulation

Compact Display of a Phylogeny

Plot Variance Components

plot.phylo.extra

Extra Fuctions to Plot and Annotate Phylogenies

Multivariate Character Simulation

Plot Phylogenies

Internal Reordering of Trees

Read DNA Sequences from GenBank via Internet

read.nexus.data

Read Character Data In NEXUS Format

Read Tree File in CAIC Format

Continuous Ancestral Character Estimation

Read Tree File in Nexus Format

richness.yule.test

Test of Diversification-Shift With the Yule Process

Read DNA Sequences in a File

Read Tree File in Parenthetic Format

Generate Random Trees

Root a Tree by Root-to-Tip Regression

slowinskiguyer.test

Slowinski-Guyer Test of Homogeneous Diversification

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

Drawing Skyline Plot Graphs

Find Segregating Sites in DNA Sequences

Skyline Plot Estimate of Effective Population Size

Roots Phylogenetic Trees

solveAmbiguousBases

Solve Ambiguous Bases in DNA Sequences

Swapping Sister Clades

Translation from DNA to Amino Acid Sequences

Tree Explorer With Multiple Devices

Print Summary of a Phylogeny

Species Tree Estimation

unique.multiPhylo

Revomes Duplicate Trees

Generates Systematic Regular Trees

Zoom on a Portion of a Phylogeny by Successive Clicks

All subtrees of a Phylogenetic Tree

Tree Reconstruction Based on the Triangles Method

Write DNA Sequences in a File

Find Patterns in DNA Sequences

Identifies Edges of a Tree

Fits the Time-Dependent Yule Model

Define Similarity Matrix

Zoom on a Portion of a Phylogeny

Variance Components with Orthonormal Contrasts

Write Tree File in Nexus Format

Variance-Covariance Matrix to Tree

Write Tree File in Parenthetic Format

Compute Variance Component Estimates

write.nexus.data

Write Character Data in NEXUS Format

Fits the Yule Model to a Phylogenetic Tree

Fits the Yule Model With Covariates

Cytochrome b Gene Sequences of Woodmice

Phylogenetic Variance-covariance or Correlation Matrix