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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

92,890

Version

5.5

License

GPL-2 | GPL-3

Maintainer

Emmanuel Paradis

Last Published

April 25th, 2021

Functions in ape (5.5)

Most Parsimonious Reconstruction

as.phylo.formula

Conversion from Taxonomy Variables to Phylogenetic Trees

Moran's I Autocorrelation Index

Alignment Explorer With Multiple Devices

Conversion Among DNA Sequence Internal Formats

Phylogenetic Generalized Linear Mixed Model for Binary Data

Time-Dependent Birth-Death Models

Tools to Explore Files

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

Ornstein--Uhlenbeck Model for Continuous Characters

Multiple Sequence Alignment with External Applications

Number of Cherries and Null Models of Trees

Compare Two "phylo" Objects

Comparative Analysis with GEEs

Axis on Side of Phylogeny

all.equal.DNAbin

Compare DNA Sets

Amino Acid Sequences

Balance of a Dichotomous Phylogenetic Tree

Congruence among distance matrices

Lynch's Comparative Method

Pagel's ``lambda'' Correlation Structure

Carnivora body sizes and life history traits

Analyses of Phylogenetics and Evolution

Internal Ape Functions

Check DNA Alignments

Molecular Dating With Penalized Likelihood

Molecular Dating With Mean Path Lengths

Base frequencies from DNA Sequences

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

Probability Density Under Birth--Death Models

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

Correlations among Multiple Traits with Phylogenetic Signal

Blomberg et al.'s Correlation Structure

Initialize.corPhyl

Initialize a `corPhyl' Structure Object

Estimation of Speciation and Extinction Rates With Birth-Death Models

Pairwise Distances from Genetic Data

Draw Additional Edges on a Plotted Tree

Pairwise Distances from DNA Sequences

Tree Bipartition and Bootstrapping Phylogenies

correlogram.formula

Phylogenetic Correlogram

NEXUS Data Example

Compute and Set Branching Times

Branch Lengths Computation

Delete Alignment Gaps in DNA Sequences

Theoretical Lineage-Through Time Plots

Print DNA or AA Sequence Alignement

all.equal.phylo

Global Comparison of two Phylogenies

Evolutionary Networks

coalescent.intervals

Coalescent Intervals

Graphical Identification of Nodes and Tips

collapse.singles

Collapse Single Nodes

Concensus Trees

Definition of Vectors for Plotting or Annotating

Conversion Between Phylo and Matching Objects

Split Frequencies and Conversion Among Split Classes

branching.times

Branching Times of a Phylogenetic Tree

Building Lists of Trees

Leading and Trailing Alignment Gaps to N

Remove Tips in a Phylogenetic Tree

Checking Labels

Ladderize a Tree

Label Management

Makes Node Labels

Construction of Consensus Distance Matrix With SDM

Tree Estimation Based on the Minimum Evolution Algorithm

Ancestral Character Estimation

Label Management

Incomplete distances and edge weights of unrooted topology

Mantel Test for Similarity of Two Matrices

Plot Multiple Chronograms on the Same Scale

cophenetic.phylo

Pairwise Distances from a Phylogenetic Tree

checkValidPhylo

Check the Structure of a "phylo" Object

Compact Display of a Phylogeny

Random DNA Sequences

Plot of DNA Sequence Alignement

Grafen's (1989) Correlation Structure

Gamma-Statistic of Pybus and Harvey

Tree Estimation Based on an Improved Version of the NJ Algorithm

getAnnotationsGenBank

Read Annotations from GenBank

Find Most Recent Common Ancestors Between Pairs

Test if a Tree is Ultrametric

is.monophyletic

Is Group Monophyletic

Matrix Exponential

mcconwaysims.test

McConway-Sims Test of Homogeneous Diversification

Minimum Variance Reduction

Martins's (1997) Correlation Structure

Topological Distances Between Two Trees

Neighbor-Joining Tree Estimation

Multiple regression through the origin

Phylogenetic Tree of 193 HIV-1 Sequences

Tests of Constant Diversification Rates

Calculate Numbers of Phylogenetic Trees

Phylogenetic Correlation Structures

compar.cheverud

Cheverud's Comparative Method

collapsed.intervals

Collapsed Coalescent Intervals

Brownian Correlation Structure

Find Paths of Nodes

Lineages Through Time Plot

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

Multivariate Character Simulation

Test of host-parasite coevolution

Analysis of Diversification with Survival Models

Read Tree File in Nexus Format

Roots Phylogenetic Trees

Root a Tree by Root-to-Tip Regression

Internal Reordering of Trees

Continuous Ancestral Character Estimation

Generate Random Trees

Read DNA Sequences from GenBank via Internet

Compute Variance Component Estimates

Swapping Sister Clades

Zoom on a Portion of a Phylogeny

Phylogenetic Variance-covariance or Correlation Matrix

Variance Components with Orthonormal Contrasts

Principal Coordinate Analysis

Variance-Covariance Matrix to Tree

Collapse and Resolve Multichotomies

Manipulating Lists of Trees

Minimum Spanning Tree

Depth and Heights of Nodes and Tips

Phylogenetically Independent Orthonormal Contrasts

plot.correlogram

Plot a Correlogram

Labelling the Nodes, Tips, and Edges of a Tree

Plot Phylogenies

Plot Tree With Time Axis

Plot Variance Components

Tree Annotation

Define Similarity Matrix

Read Tree File in CAIC Format

Continuous Character Simulation

Discrete Character Simulation

read.nexus.data

Read Character Data In NEXUS Format

Zoom on a Portion of a Phylogeny by Successive Clicks

Read DNA Sequences in a File

diversity.contrast.test

Diversity Contrast Test

Read Tree File in Parenthetic Format

Check Compatibility of Splits

Test for Binary Tree

All subtrees of a Phylogenetic Tree

Write Tree File in Nexus Format

write.nexus.data

Write Character Data in NEXUS Format

Fits the Yule Model With Covariates

Fits the Time-Dependent Yule Model

plot.phylo.extra

Extra Fuctions to Plot and Annotate Phylogenies

Find Segregating Sites in DNA Sequences

Skyline Plot Estimate of Effective Population Size

Five Independent Trees

Drawing Skyline Plot Graphs

slowinskiguyer.test

Slowinski-Guyer Test of Homogeneous Diversification

Tree Explorer With Multiple Devices

Print Summary of a Phylogeny

Translation from DNA to Amino Acid Sequences

Mixed Font Labels for Plotting

Fits a Bunch of Models with PhyML

Reversible Jump MCMC to Infer Demographic History

Find Patterns in DNA Sequences

Phylogenetically Independent Contrasts

Identifies Edges of a Tree

Fits the Yule Model to a Phylogenetic Tree

Write Tree File in Parenthetic Format

richness.yule.test

Test of Diversification-Shift With the Yule Process

Species Tree Estimation

Generates Systematic Regular Trees

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

Tree Reconstruction Based on the Triangles Method

unique.multiPhylo

Revomes Duplicate Trees

Cytochrome b Gene Sequences of Woodmice

Write DNA Sequences in a File

Recode Blocks of Indels

Manipulate DNA Sequences in Bit-Level Format

Add a Scale Bar to a Phylogeny Plot

Incomplete Distance Matrix Filling

Conversion Among Tree and Network Objects