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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

5.7-1

License

GPL-2 | GPL-3

Issues

Pull Requests

Stars

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Repository

https://github.com/emmanuelparadis/ape

Homepage

http://ape-package.ird.fr/

Maintainer

Emmanuel Paradis

Last Published

March 13th, 2023

Functions in ape (5.7-1)

Ancestral Character Estimation

Tools to Explore Files

Conversion Among DNA Sequence Internal Formats

Conversion Among Tree and Network Objects

as.phylo.formula

Conversion from Taxonomy Variables to Phylogenetic Trees

Recode Blocks of Indels

Add a Scale Bar to a Phylogeny Plot

Incomplete Distance Matrix Filling

Split Frequencies and Conversion Among Split Classes

Conversion Between Phylo and Matching Objects

Molecular Dating by Penalised Likelihood and Maximum Likelihood

Phylogeny of the Families of Birds From Sibley and Ahlquist

Multiple Sequence Alignment with External Applications

Most Parsimonious Reconstruction

Ornstein--Uhlenbeck Model for Continuous Characters

Compare Two "phylo" Objects

Axis on Side of Phylogeny

Amino Acid Sequences

Phylogeny of the Orders of Birds From Sibley and Ahlquist

Balance of a Dichotomous Phylogenetic Tree

Congruence among distance matrices

branching.times

Branching Times of a Phylogenetic Tree

Moran's I Autocorrelation Index

Pagel's ``lambda'' Correlation Structure

collapsed.intervals

Collapsed Coalescent Intervals

Correlations among Multiple Traits with Phylogenetic Signal

compar.cheverud

Cheverud's Comparative Method

all.equal.phylo

Global Comparison of two Phylogenies

Initialize.corPhyl

Initialize a `corPhyl' Structure Object

Grafen's (1989) Correlation Structure

Internal Ape Functions

Theoretical Lineage-Through Time Plots

Building Lists of Trees

Print DNA or AA Sequence Alignement

Analyses of Phylogenetics and Evolution

Alignment Explorer With Multiple Devices

Carnivora body sizes and life history traits

Check DNA Alignments

Tests of Constant Diversification Rates

Time-Dependent Birth-Death Models

all.equal.DNAbin

Compare DNA Sets

coalescent.intervals

Coalescent Intervals

Phylogenetic Generalized Linear Mixed Model for Binary Data

Base frequencies from DNA Sequences

Number of Cherries and Null Models of Trees

Martins's (1997) Correlation Structure

Analysis of Diversification with Survival Models

diversity.contrast.test

Diversity Contrast Test

Tree Estimation Based on an Improved Version of the NJ Algorithm

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

Pairwise Distances from DNA Sequences

Estimation of Speciation and Extinction Rates With Birth-Death Models

collapse.singles

Collapse Single Nodes

getAnnotationsGenBank

Read Annotations from GenBank

Concensus Trees

Phylogenetic Tree of 193 HIV-1 Sequences

Tree Estimation Based on the Minimum Evolution Algorithm

cophenetic.phylo

Pairwise Distances from a Phylogenetic Tree

Gamma-Statistic of Pybus and Harvey

Lineages Through Time Plot

Label Management

Brownian Correlation Structure

Tree Bipartition and Bootstrapping Phylogenies

Label Management

Phylogenetic Correlation Structures

Checking Labels

Test of host-parasite coevolution

Probability Density Under Birth--Death Models

Ladderize a Tree

Check Compatibility of Splits

Definition of Vectors for Plotting or Annotating

checkValidPhylo

Check the Structure of a "phylo" Object

Branch Lengths Computation

Remove Tips in a Phylogenetic Tree

Compute and Set Branching Times

is.monophyletic

Is Group Monophyletic

Makes Node Labels

Mantel Test for Similarity of Two Matrices

Molecular Dating With Mean Path Lengths

correlogram.formula

Phylogenetic Correlogram

Principal Coordinate Analysis

Draw Additional Edges on a Plotted Tree

Molecular Dating With Penalized Likelihood

NEXUS Data Example

Comparative Analysis with GEEs

Random DNA Sequences

Lynch's Comparative Method

Continuous Character Simulation

Manipulating Lists of Trees

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

Swapping Sister Clades

Pairwise Distances from Genetic Data

Blomberg et al.'s Correlation Structure

Plot of DNA Sequence Alignement

Generate Random Trees

Vertex Degrees in Trees and Networks

Compute Variance Component Estimates

Minimum Variance Reduction

Test for Binary Tree

Phylogenetic Variance-covariance or Correlation Matrix

Delete Alignment Gaps in DNA Sequences

Tree Annotation

Fits a Bunch of Models with PhyML

Topological Distances Between Two Trees

Minimum Spanning Tree

Discrete Character Simulation

Test if a Tree is Ultrametric

Multivariate Character Simulation

Plot Multiple Chronograms on the Same Scale

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

Neighbor-Joining Tree Estimation

Evolutionary Networks

Phylogenetically Independent Contrasts

Collapse and Resolve Multichotomies

Incomplete distances and edge weights of unrooted topology

Calculate Numbers of Phylogenetic Trees

plot.correlogram

Plot a Correlogram

Phylogenetically Independent Orthonormal Contrasts

Internal Reordering of Trees

Graphical Identification of Nodes and Tips

Plot Phylogenies

Plot Tree With Time Axis

richness.yule.test

Test of Diversification-Shift With the Yule Process

Read Tree File in Parenthetic Format

slowinskiguyer.test

Slowinski-Guyer Test of Homogeneous Diversification

Five Independent Trees

Compact Display of a Phylogeny

solveAmbiguousBases

Solve Ambiguous Bases in DNA Sequences

Matrix Exponential

mcconwaysims.test

McConway-Sims Test of Homogeneous Diversification

Reversible Jump MCMC to Infer Demographic History

Continuous Ancestral Character Estimation

Skyline Plot Estimate of Effective Population Size

Read DNA Sequences in a File

Leading and Trailing Alignment Gaps to N

Depth and Heights of Nodes and Tips

Multiple regression through the origin

plot.phylo.extra

Extra Fuctions to Plot and Annotate Phylogenies

Drawing Skyline Plot Graphs

Zoom on a Portion of a Phylogeny by Successive Clicks

Mixed Font Labels for Plotting

Tree Explorer With Multiple Devices

Tree Reconstruction Based on the Triangles Method

Write Tree File in Parenthetic Format

Find Most Recent Common Ancestors Between Pairs

All subtrees of a Phylogenetic Tree

Fits the Yule Model to a Phylogenetic Tree

Labelling the Nodes, Tips, and Edges of a Tree

Plot Variance Components

Variance Components with Orthonormal Contrasts

Find Paths of Nodes

unique.multiPhylo

Revomes Duplicate Trees

Read DNA Sequences from GenBank via Internet

Find Patterns in DNA Sequences

Identifies Edges of a Tree

Read Tree File in CAIC Format

Read Tree File in Nexus Format

read.nexus.data

Read Character Data In NEXUS Format

Root a Tree by Root-to-Tip Regression

Zoom on a Portion of a Phylogeny

Find Segregating Sites in DNA Sequences

Print Summary of a Phylogeny

Translation from DNA to Amino Acid Sequences

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

Variance-Covariance Matrix to Tree

Define Similarity Matrix

Fits the Yule Model With Covariates

Fits the Time-Dependent Yule Model

Roots Phylogenetic Trees

Species Tree Estimation

Generates Systematic Regular Trees

Cytochrome b Gene Sequences of Woodmice

Write DNA Sequences in a File

Write Tree File in Nexus Format

write.nexus.data

Write Character Data in NEXUS Format

Construction of Consensus Distance Matrix With SDM

Manipulate DNA Sequences in Bit-Level Format