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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

5.6-1

License

GPL-2 | GPL-3

Maintainer

Emmanuel Paradis

Last Published

January 7th, 2022

Functions in ape (5.6-1)

Manipulate DNA Sequences in Bit-Level Format

Construction of Consensus Distance Matrix With SDM

Amino Acid Sequences

Ancestral Character Estimation

Most Parsimonious Reconstruction

Moran's I Autocorrelation Index

Theoretical Lineage-Through Time Plots

Recode Blocks of Indels

Congruence among distance matrices

Initialize.corPhyl

Initialize a `corPhyl' Structure Object

all.equal.phylo

Global Comparison of two Phylogenies

Print DNA or AA Sequence Alignement

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

Add a Scale Bar to a Phylogeny Plot

Axis on Side of Phylogeny

Tools to Explore Files

Balance of a Dichotomous Phylogenetic Tree

Base frequencies from DNA Sequences

Estimation of Speciation and Extinction Rates With Birth-Death Models

Carnivora body sizes and life history traits

Conversion Among Tree and Network Objects

as.phylo.formula

Conversion from Taxonomy Variables to Phylogenetic Trees

Conversion Among DNA Sequence Internal Formats

Internal Ape Functions

all.equal.DNAbin

Compare DNA Sets

Alignment Explorer With Multiple Devices

Split Frequencies and Conversion Among Split Classes

Conversion Between Phylo and Matching Objects

Analyses of Phylogenetics and Evolution

Incomplete Distance Matrix Filling

Time-Dependent Birth-Death Models

coalescent.intervals

Coalescent Intervals

collapse.singles

Collapse Single Nodes

correlogram.formula

Phylogenetic Correlogram

Compare Two "phylo" Objects

Ornstein--Uhlenbeck Model for Continuous Characters

NEXUS Data Example

branching.times

Branching Times of a Phylogenetic Tree

Phylogenetic Generalized Linear Mixed Model for Binary Data

Phylogeny of the Orders of Birds From Sibley and Ahlquist

Phylogeny of the Families of Birds From Sibley and Ahlquist

Check DNA Alignments

Tree Bipartition and Bootstrapping Phylogenies

Lynch's Comparative Method

Building Lists of Trees

Comparative Analysis with GEEs

Checking Labels

Branch Lengths Computation

checkValidPhylo

Check the Structure of a "phylo" Object

Evolutionary Networks

Tree Estimation Based on an Improved Version of the NJ Algorithm

Tests of Constant Diversification Rates

Molecular Dating by Penalised Likelihood and Maximum Likelihood

Number of Cherries and Null Models of Trees

Compute and Set Branching Times

Grafen's (1989) Correlation Structure

collapsed.intervals

Collapsed Coalescent Intervals

Blomberg et al.'s Correlation Structure

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

compar.cheverud

Cheverud's Comparative Method

Martins's (1997) Correlation Structure

Molecular Dating With Mean Path Lengths

Molecular Dating With Penalized Likelihood

Incomplete distances and edge weights of unrooted topology

Pagel's ``lambda'' Correlation Structure

Analysis of Diversification with Survival Models

Plot Multiple Chronograms on the Same Scale

Test if a Tree is Ultrametric

Neighbor-Joining Tree Estimation

Labelling the Nodes, Tips, and Edges of a Tree

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

Find Paths of Nodes

Multiple Sequence Alignment with External Applications

Pairwise Distances from Genetic Data

Discrete Character Simulation

cophenetic.phylo

Pairwise Distances from a Phylogenetic Tree

Brownian Correlation Structure

Concensus Trees

Tree Estimation Based on the Minimum Evolution Algorithm

Phylogenetic Correlation Structures

Definition of Vectors for Plotting or Annotating

Probability Density Under Birth--Death Models

Pairwise Distances from DNA Sequences

diversity.contrast.test

Diversity Contrast Test

Vertex Degrees in Trees and Networks

Correlations among Multiple Traits with Phylogenetic Signal

getAnnotationsGenBank

Read Annotations from GenBank

Topological Distances Between Two Trees

Gamma-Statistic of Pybus and Harvey

Manipulating Lists of Trees

Plot of DNA Sequence Alignement

Makes Node Labels

Mantel Test for Similarity of Two Matrices

Test for Binary Tree

Multivariate Character Simulation

Minimum Variance Reduction

Check Compatibility of Splits

is.monophyletic

Is Group Monophyletic

Phylogenetic Tree of 193 HIV-1 Sequences

Phylogenetically Independent Contrasts

Plot Tree With Time Axis

Lineages Through Time Plot

Test of host-parasite coevolution

Principal Coordinate Analysis

Label Management

mcconwaysims.test

McConway-Sims Test of Homogeneous Diversification

Reversible Jump MCMC to Infer Demographic History

Delete Alignment Gaps in DNA Sequences

Graphical Identification of Nodes and Tips

Calculate Numbers of Phylogenetic Trees

Compact Display of a Phylogeny

Internal Reordering of Trees

Remove Tips in a Phylogenetic Tree

Label Management

Skyline Plot Estimate of Effective Population Size

All subtrees of a Phylogenetic Tree

richness.yule.test

Test of Diversification-Shift With the Yule Process

Drawing Skyline Plot Graphs

Species Tree Estimation

Zoom on a Portion of a Phylogeny by Successive Clicks

Multiple regression through the origin

Leading and Trailing Alignment Gaps to N

Phylogenetically Independent Orthonormal Contrasts

Plot Variance Components

plot.phylo.extra

Extra Fuctions to Plot and Annotate Phylogenies

Ladderize a Tree

Find Most Recent Common Ancestors Between Pairs

Draw Additional Edges on a Plotted Tree

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

Read DNA Sequences in a File

Mixed Font Labels for Plotting

Five Independent Trees

Roots Phylogenetic Trees

Matrix Exponential

Generates Systematic Regular Trees

Minimum Spanning Tree

read.nexus.data

Read Character Data In NEXUS Format

Read Tree File in Nexus Format

Identifies Edges of a Tree

Depth and Heights of Nodes and Tips

Find Patterns in DNA Sequences

Zoom on a Portion of a Phylogeny

Tree Reconstruction Based on the Triangles Method

unique.multiPhylo

Revomes Duplicate Trees

Collapse and Resolve Multichotomies

Variance-Covariance Matrix to Tree

solveAmbiguousBases

Solve Ambiguous Bases in DNA Sequences

Tree Annotation

slowinskiguyer.test

Slowinski-Guyer Test of Homogeneous Diversification

Fits a Bunch of Models with PhyML

Continuous Character Simulation

Random DNA Sequences

Tree Explorer With Multiple Devices

Define Similarity Matrix

Cytochrome b Gene Sequences of Woodmice

Fits the Yule Model to a Phylogenetic Tree

Write DNA Sequences in a File

Write Tree File in Parenthetic Format

Root a Tree by Root-to-Tip Regression

Read DNA Sequences from GenBank via Internet

Plot Phylogenies

Continuous Ancestral Character Estimation

plot.correlogram

Plot a Correlogram

Read Tree File in CAIC Format

Read Tree File in Parenthetic Format

Swapping Sister Clades

Generate Random Trees

Find Segregating Sites in DNA Sequences

Variance Components with Orthonormal Contrasts

write.nexus.data

Write Character Data in NEXUS Format

Write Tree File in Nexus Format

Print Summary of a Phylogeny

Translation from DNA to Amino Acid Sequences

Fits the Yule Model With Covariates

Fits the Time-Dependent Yule Model

Compute Variance Component Estimates

Phylogenetic Variance-covariance or Correlation Matrix