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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

101,907

Version

5.6

License

GPL-2 | GPL-3

Maintainer

Emmanuel Paradis

Last Published

December 21st, 2021

Functions in ape (5.6)

Amino Acid Sequences

Congruence among distance matrices

Initialize.corPhyl

Initialize a `corPhyl' Structure Object

Most Parsimonious Reconstruction

Moran's I Autocorrelation Index

all.equal.phylo

Global Comparison of two Phylogenies

Print DNA or AA Sequence Alignement

Incomplete Distance Matrix Filling

Theoretical Lineage-Through Time Plots

Add a Scale Bar to a Phylogeny Plot

Analyses of Phylogenetics and Evolution

Internal Ape Functions

Tools to Explore Files

Conversion Among DNA Sequence Internal Formats

Phylogenetic Generalized Linear Mixed Model for Binary Data

Time-Dependent Birth-Death Models

Conversion Among Tree and Network Objects

as.phylo.formula

Conversion from Taxonomy Variables to Phylogenetic Trees

Construction of Consensus Distance Matrix With SDM

Conversion Between Phylo and Matching Objects

all.equal.DNAbin

Compare DNA Sets

Ancestral Character Estimation

Alignment Explorer With Multiple Devices

Axis on Side of Phylogeny

Split Frequencies and Conversion Among Split Classes

Balance of a Dichotomous Phylogenetic Tree

branching.times

Branching Times of a Phylogenetic Tree

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

Recode Blocks of Indels

Manipulate DNA Sequences in Bit-Level Format

Base frequencies from DNA Sequences

Building Lists of Trees

Phylogeny of the Orders of Birds From Sibley and Ahlquist

Phylogeny of the Families of Birds From Sibley and Ahlquist

Molecular Dating by Penalised Likelihood and Maximum Likelihood

Tree Bipartition and Bootstrapping Phylogenies

Estimation of Speciation and Extinction Rates With Birth-Death Models

Multiple Sequence Alignment with External Applications

checkValidPhylo

Check the Structure of a "phylo" Object

Checking Labels

Carnivora body sizes and life history traits

Check DNA Alignments

coalescent.intervals

Coalescent Intervals

collapse.singles

Collapse Single Nodes

Lynch's Comparative Method

Comparative Analysis with GEEs

Number of Cherries and Null Models of Trees

Compute and Set Branching Times

Branch Lengths Computation

compar.cheverud

Cheverud's Comparative Method

collapsed.intervals

Collapsed Coalescent Intervals

Concensus Trees

cophenetic.phylo

Pairwise Distances from a Phylogenetic Tree

Molecular Dating With Penalized Likelihood

Tree Estimation Based on an Improved Version of the NJ Algorithm

Ornstein--Uhlenbeck Model for Continuous Characters

Molecular Dating With Mean Path Lengths

Pagel's ``lambda'' Correlation Structure

Correlations among Multiple Traits with Phylogenetic Signal

Brownian Correlation Structure

Phylogenetic Correlation Structures

Compare Two "phylo" Objects

Grafen's (1989) Correlation Structure

Martins's (1997) Correlation Structure

Blomberg et al.'s Correlation Structure

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

correlogram.formula

Phylogenetic Correlogram

NEXUS Data Example

Definition of Vectors for Plotting or Annotating

Probability Density Under Birth--Death Models

Pairwise Distances from DNA Sequences

Delete Alignment Gaps in DNA Sequences

Vertex Degrees in Trees and Networks

Topological Distances Between Two Trees

Pairwise Distances from Genetic Data

Analysis of Diversification with Survival Models

Tests of Constant Diversification Rates

Remove Tips in a Phylogenetic Tree

diversity.contrast.test

Diversity Contrast Test

getAnnotationsGenBank

Read Annotations from GenBank

Tree Estimation Based on the Minimum Evolution Algorithm

Draw Additional Edges on a Plotted Tree

Phylogenetic Tree of 193 HIV-1 Sequences

Evolutionary Networks

Gamma-Statistic of Pybus and Harvey

Incomplete distances and edge weights of unrooted topology

Label Management

Check Compatibility of Splits

Calculate Numbers of Phylogenetic Trees

Graphical Identification of Nodes and Tips

Test for Binary Tree

Plot of DNA Sequence Alignement

is.monophyletic

Is Group Monophyletic

Ladderize a Tree

Plot Multiple Chronograms on the Same Scale

Test if a Tree is Ultrametric

Leading and Trailing Alignment Gaps to N

Matrix Exponential

Five Independent Trees

Multiple regression through the origin

Label Management

Find Most Recent Common Ancestors Between Pairs

Mixed Font Labels for Plotting

Lineages Through Time Plot

mcconwaysims.test

McConway-Sims Test of Homogeneous Diversification

Reversible Jump MCMC to Infer Demographic History

Neighbor-Joining Tree Estimation

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

Collapse and Resolve Multichotomies

Mantel Test for Similarity of Two Matrices

Makes Node Labels

Minimum Spanning Tree

Manipulating Lists of Trees

Minimum Variance Reduction

Labelling the Nodes, Tips, and Edges of a Tree

Test of host-parasite coevolution

Fits a Bunch of Models with PhyML

Tree Annotation

Principal Coordinate Analysis

Phylogenetically Independent Orthonormal Contrasts

Phylogenetically Independent Contrasts

Find Paths of Nodes

Depth and Heights of Nodes and Tips

Discrete Character Simulation

Multivariate Character Simulation

Plot Tree With Time Axis

Continuous Character Simulation

plot.correlogram

Plot a Correlogram

plot.phylo.extra

Extra Fuctions to Plot and Annotate Phylogenies

Random DNA Sequences

Plot Phylogenies

Compact Display of a Phylogeny

Plot Variance Components

Read Tree File in Parenthetic Format

richness.yule.test

Test of Diversification-Shift With the Yule Process

Internal Reordering of Trees

Continuous Ancestral Character Estimation

Read DNA Sequences in a File

Read DNA Sequences from GenBank via Internet

Read Tree File in CAIC Format

read.nexus.data

Read Character Data In NEXUS Format

Read Tree File in Nexus Format

Root a Tree by Root-to-Tip Regression

slowinskiguyer.test

Slowinski-Guyer Test of Homogeneous Diversification

Drawing Skyline Plot Graphs

Generate Random Trees

solveAmbiguousBases

Solve Ambiguous Bases in DNA Sequences

Skyline Plot Estimate of Effective Population Size

Swapping Sister Clades

Find Segregating Sites in DNA Sequences

Roots Phylogenetic Trees

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

Tree Reconstruction Based on the Triangles Method

Print Summary of a Phylogeny

Tree Explorer With Multiple Devices

Translation from DNA to Amino Acid Sequences

unique.multiPhylo

Revomes Duplicate Trees

Generates Systematic Regular Trees

Species Tree Estimation

Zoom on a Portion of a Phylogeny by Successive Clicks

All subtrees of a Phylogenetic Tree

Define Similarity Matrix

Identifies Edges of a Tree

Find Patterns in DNA Sequences

Variance-Covariance Matrix to Tree

Variance Components with Orthonormal Contrasts

Phylogenetic Variance-covariance or Correlation Matrix

Compute Variance Component Estimates

Cytochrome b Gene Sequences of Woodmice

Write DNA Sequences in a File

Fits the Time-Dependent Yule Model

write.nexus.data

Write Character Data in NEXUS Format

Zoom on a Portion of a Phylogeny

Fits the Yule Model to a Phylogenetic Tree

Fits the Yule Model With Covariates

Write Tree File in Parenthetic Format

Write Tree File in Nexus Format