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ape

This is the development version of ape.

To know more about ape: https://emmanuelparadis.github.io

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Install

install.packages('ape')

Monthly Downloads

92,890

Version

5.8-1

License

GPL-2 | GPL-3

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Repository

https://github.com/emmanuelparadis/ape

Maintainer

Emmanuel Paradis

Last Published

December 16th, 2024

Functions in ape (5.8-1)

Balance of a Dichotomous Phylogenetic Tree

Base frequencies from DNA Sequences

Tree Estimation Based on an Improved Version of the NJ Algorithm

Add a Scale Bar to a Phylogeny Plot

Building Lists of Trees

Phylogeny of the Families of Birds From Sibley and Ahlquist

Time-Dependent Birth-Death Models

Phylogeny of the Orders of Birds From Sibley and Ahlquist

Incomplete Distance Matrix Filling

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

branching.times

Branching Times of a Phylogenetic Tree

Phylogenetic Generalized Linear Mixed Model for Binary Data

Tree Bipartition and Bootstrapping Phylogenies

Molecular Dating With Penalized Likelihood

Estimation of Speciation and Extinction Rates With Birth-Death Models

Carnivora body sizes and life history traits

Molecular Dating by Penalised Likelihood and Maximum Likelihood

Multiple Sequence Alignment with External Applications

Molecular Dating With Mean Path Lengths

Ornstein--Uhlenbeck Model for Continuous Characters

Comparative Analysis with GEEs

Compare Two "phylo" Objects

Checking Labels

Tools to Explore Files

Lynch's Comparative Method

Check DNA Alignments

checkValidPhylo

Check the Structure of a "phylo" Object

coalescent.intervals

Coalescent Intervals

Conversion Between Phylo and Matching Objects

collapsed.intervals

Collapsed Coalescent Intervals

Conversion Among DNA Sequence Internal Formats

Split Frequencies and Conversion Among Split Classes

collapse.singles

Collapse Single Nodes

Concensus Trees

Number of Cherries and Null Models of Trees

cophenetic.phylo

Pairwise Distances from a Phylogenetic Tree

Compute and Set Branching Times

Branch Lengths Computation

Brownian Correlation Structure

Grafen's (1989) Correlation Structure

Martins's (1997) Correlation Structure

Phylogenetic Correlation Structures

Correlations among Multiple Traits with Phylogenetic Signal

compar.cheverud

Cheverud's Comparative Method

Blomberg et al.'s Correlation Structure

correlogram.formula

Phylogenetic Correlogram

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

Pagel's ``lambda'' Correlation Structure

NEXUS Data Example

Pairwise Distances from Genetic Data

Tests of Constant Diversification Rates

Vertex Degrees in Trees and Networks

Analysis of Diversification with Survival Models

Delete Alignment Gaps in DNA or AA Sequences

Topological Distances Between Two Trees

Incomplete distances and edge weights of unrooted topology

Gamma-Statistic of Pybus and Harvey

Probability Density Under Birth--Death Models

Definition of Vectors for Plotting or Annotating

Draw Additional Edges on a Plotted Tree

Phylogenetic Tree of 193 HIV-1 Sequences

Tree Estimation Based on the Minimum Evolution Algorithm

Remove Tips in a Phylogenetic Tree

getAnnotationsGenBank

Read Annotations from GenBank

Evolutionary Networks

Pairwise Distances from DNA Sequences

Plot Multiple Chronograms on the Same Scale

Label Management

Test if a Tree is Ultrametric

Ladderize a Tree

diversity.contrast.test

Diversity Contrast Test

Calculate Numbers of Phylogenetic Trees

Plot of DNA Sequence Alignement

is.monophyletic

Is Group Monophyletic

Test for Binary Tree

Check Compatibility of Splits

Graphical Identification of Nodes and Tips

Lineages Through Time Plot

Multiple regression through the origin

Leading and Trailing Alignment Gaps to N

mcconwaysims.test

McConway-Sims Test of Homogeneous Diversification

Minimum Spanning Tree

Reversible Jump MCMC to Infer Demographic History

Five Independent Trees

Mantel Test for Similarity of Two Matrices

Matrix Exponential

Collapse and Resolve Multichotomies

Makes Node Labels

Minimum Variance Reduction

Manipulating Lists of Trees

Neighbor-Joining Tree Estimation

Label Management

Mixed Font Labels for Plotting

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

Find Most Recent Common Ancestors Between Pairs

Phylogenetically Independent Contrasts

Depth and Heights of Nodes and Tips

Phylogenetically Independent Orthonormal Contrasts

Test of host-parasite coevolution

Labelling the Nodes, Tips, and Edges of a Tree

Find Paths of Nodes

Principal Coordinate Analysis

plot.phylo.extra

Extra Fuctions to Plot and Annotate Phylogenies

Plot Tree With Time Axis

Fits a Bunch of Models with PhyML

Tree Annotation

Random DNA Sequences

Compact Display of a Phylogeny

Plot Phylogenies

plot.correlogram

Plot a Correlogram

Continuous Character Simulation

Multivariate Character Simulation

Discrete Character Simulation

Plot Variance Components

Read Tree File in Parenthetic Format

Read DNA Sequences from GenBank via Internet

Read Tree File in CAIC Format

Internal Reordering of Trees

Continuous Ancestral Character Estimation

slowinskiguyer.test

Slowinski-Guyer Test of Homogeneous Diversification

richness.yule.test

Test of Diversification-Shift With the Yule Process

solveAmbiguousBases

Solve Ambiguous Bases in DNA Sequences

Species Tree Estimation

Generates Systematic Regular Trees

Read Tree File in Nexus Format

read.nexus.data

Read Character Data In NEXUS Format

Tree Explorer With Multiple Devices

Read DNA Sequences in a File

Root a Tree by Root-to-Tip Regression

Skyline Plot Estimate of Effective Population Size

Zoom on a Portion of a Phylogeny by Successive Clicks

Cytochrome b Gene Sequences of Woodmice

Find Segregating Sites in DNA Sequences

Swapping Sister Clades

Write DNA Sequences in a File

Roots Phylogenetic Trees

Drawing Skyline Plot Graphs

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

Fits the Yule Model to a Phylogenetic Tree

Generate Random Trees

Zoom on a Portion of a Phylogeny

Fits the Time-Dependent Yule Model

Fits the Yule Model With Covariates

All subtrees of a Phylogenetic Tree

Print Summary of a Phylogeny

Find Patterns in DNA Sequences

Identifies Edges of a Tree

Tree Reconstruction Based on the Triangles Method

Translation from DNA to Amino Acid Sequences

Compute Variance Component Estimates

Phylogenetic Variance-covariance or Correlation Matrix

unique.multiPhylo

Revomes Duplicate Trees

Variance-Covariance Matrix to Tree

Write Tree File in phyloXML Format

Variance Components with Orthonormal Contrasts

Define Similarity Matrix

Write Tree File in Nexus Format

Write Tree File in Parenthetic Format

write.nexus.data

Write Character Data in NEXUS Format

Recode Blocks of Indels

Analyses of Phylogenetics and Evolution

Alignment Explorer With Multiple Devices

Amino Acid Sequences

Most Parsimonious Reconstruction

all.equal.phylo

Global Comparison of two Phylogenies

Theoretical Lineage-Through Time Plots

all.equal.DNAbin

Compare DNA Sets

Manipulate DNA Sequences in Bit-Level Format

Ancestral Character Estimation

Congruence among distance matrices

Initialize.corPhyl

Initialize a `corPhyl' Structure Object

Construction of Consensus Distance Matrix With SDM

Internal Ape Functions

Axis on Side of Phylogeny

Moran's I Autocorrelation Index

Print DNA or AA Sequence Alignement

Conversion Among Tree and Network Objects

as.phylo.formula

Conversion from Taxonomy Variables to Phylogenetic Trees