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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

94,730

Version

5.8

License

GPL-2 | GPL-3

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Repository

https://github.com/emmanuelparadis/ape

Maintainer

Emmanuel Paradis

Last Published

April 11th, 2024

Functions in ape (5.8)

Construction of Consensus Distance Matrix With SDM

Amino Acid Sequences

Congruence among distance matrices

Ancestral Character Estimation

Initialize.corPhyl

Initialize a `corPhyl' Structure Object

all.equal.phylo

Global Comparison of two Phylogenies

Print DNA or AA Sequence Alignement

Manipulate DNA Sequences in Bit-Level Format

Recode Blocks of Indels

Time-Dependent Birth-Death Models

Tools to Explore Files

Alignment Explorer With Multiple Devices

Phylogenetic Generalized Linear Mixed Model for Binary Data

Conversion Among DNA Sequence Internal Formats

Base frequencies from DNA Sequences

Theoretical Lineage-Through Time Plots

Internal Ape Functions

Analyses of Phylogenetics and Evolution

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

Phylogeny of the Families of Birds From Sibley and Ahlquist

Carnivora body sizes and life history traits

Phylogeny of the Orders of Birds From Sibley and Ahlquist

Check DNA Alignments

Most Parsimonious Reconstruction

Molecular Dating With Mean Path Lengths

Molecular Dating With Penalized Likelihood

Checking Labels

Ornstein--Uhlenbeck Model for Continuous Characters

Compare Two "phylo" Objects

Moran's I Autocorrelation Index

checkValidPhylo

Check the Structure of a "phylo" Object

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

Add a Scale Bar to a Phylogeny Plot

Branch Lengths Computation

Blomberg et al.'s Correlation Structure

all.equal.DNAbin

Compare DNA Sets

Compute and Set Branching Times

Pagel's ``lambda'' Correlation Structure

Correlations among Multiple Traits with Phylogenetic Signal

Conversion Among Tree and Network Objects

Tests of Constant Diversification Rates

Incomplete Distance Matrix Filling

Pairwise Distances from DNA Sequences

getAnnotationsGenBank

Read Annotations from GenBank

Axis on Side of Phylogeny

Split Frequencies and Conversion Among Split Classes

Analysis of Diversification with Survival Models

Balance of a Dichotomous Phylogenetic Tree

Phylogenetic Tree of 193 HIV-1 Sequences

Label Management

Conversion Between Phylo and Matching Objects

as.phylo.formula

Conversion from Taxonomy Variables to Phylogenetic Trees

Ladderize a Tree

Estimation of Speciation and Extinction Rates With Birth-Death Models

Lineages Through Time Plot

Tree Bipartition and Bootstrapping Phylogenies

Remove Tips in a Phylogenetic Tree

Label Management

Draw Additional Edges on a Plotted Tree

Molecular Dating by Penalised Likelihood and Maximum Likelihood

Plot of DNA Sequence Alignement

Test for Binary Tree

Leading and Trailing Alignment Gaps to N

Tree Estimation Based on an Improved Version of the NJ Algorithm

Mixed Font Labels for Plotting

coalescent.intervals

Coalescent Intervals

Multiple Sequence Alignment with External Applications

Find Most Recent Common Ancestors Between Pairs

branching.times

Branching Times of a Phylogenetic Tree

collapse.singles

Collapse Single Nodes

Comparative Analysis with GEEs

Phylogenetically Independent Contrasts

Lynch's Comparative Method

Grafen's (1989) Correlation Structure

Multiple regression through the origin

Martins's (1997) Correlation Structure

collapsed.intervals

Collapsed Coalescent Intervals

compar.cheverud

Cheverud's Comparative Method

correlogram.formula

Phylogenetic Correlogram

Vertex Degrees in Trees and Networks

NEXUS Data Example

Phylogenetically Independent Orthonormal Contrasts

Building Lists of Trees

Probability Density Under Birth--Death Models

Number of Cherries and Null Models of Trees

Plot Tree With Time Axis

Definition of Vectors for Plotting or Annotating

Compact Display of a Phylogeny

Neighbor-Joining Tree Estimation

Delete Alignment Gaps in DNA or AA Sequences

Tree Estimation Based on the Minimum Evolution Algorithm

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

diversity.contrast.test

Diversity Contrast Test

Gamma-Statistic of Pybus and Harvey

Labelling the Nodes, Tips, and Edges of a Tree

Check Compatibility of Splits

Calculate Numbers of Phylogenetic Trees

Graphical Identification of Nodes and Tips

Find Paths of Nodes

is.monophyletic

Is Group Monophyletic

plot.phylo.extra

Extra Fuctions to Plot and Annotate Phylogenies

Plot Variance Components

Makes Node Labels

Read DNA Sequences from GenBank via Internet

Read Tree File in CAIC Format

Internal Reordering of Trees

Mantel Test for Similarity of Two Matrices

Minimum Spanning Tree

richness.yule.test

Test of Diversification-Shift With the Yule Process

Collapse and Resolve Multichotomies

Concensus Trees

cophenetic.phylo

Pairwise Distances from a Phylogenetic Tree

Brownian Correlation Structure

Test of host-parasite coevolution

Phylogenetic Correlation Structures

Principal Coordinate Analysis

Pairwise Distances from Genetic Data

Skyline Plot Estimate of Effective Population Size

mcconwaysims.test

McConway-Sims Test of Homogeneous Diversification

Reversible Jump MCMC to Infer Demographic History

Drawing Skyline Plot Graphs

Topological Distances Between Two Trees

Evolutionary Networks

Incomplete distances and edge weights of unrooted topology

Test if a Tree is Ultrametric

Zoom on a Portion of a Phylogeny by Successive Clicks

All subtrees of a Phylogenetic Tree

Depth and Heights of Nodes and Tips

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

Roots Phylogenetic Trees

Discrete Character Simulation

Random DNA Sequences

Plot Multiple Chronograms on the Same Scale

Continuous Character Simulation

Multivariate Character Simulation

Read Tree File in Nexus Format

read.nexus.data

Read Character Data In NEXUS Format

Five Independent Trees

Variance Components with Orthonormal Contrasts

Root a Tree by Root-to-Tip Regression

Read DNA Sequences in a File

Matrix Exponential

Manipulating Lists of Trees

Tree Explorer With Multiple Devices

Find Segregating Sites in DNA Sequences

Minimum Variance Reduction

Tree Annotation

slowinskiguyer.test

Slowinski-Guyer Test of Homogeneous Diversification

solveAmbiguousBases

Solve Ambiguous Bases in DNA Sequences

Species Tree Estimation

Generates Systematic Regular Trees

Cytochrome b Gene Sequences of Woodmice

Write DNA Sequences in a File

Fits a Bunch of Models with PhyML

Write Tree File in Nexus Format

plot.correlogram

Plot a Correlogram

Print Summary of a Phylogeny

Plot Phylogenies

Translation from DNA to Amino Acid Sequences

Variance-Covariance Matrix to Tree

Read Tree File in Parenthetic Format

Define Similarity Matrix

Zoom on a Portion of a Phylogeny

Continuous Ancestral Character Estimation

write.nexus.data

Write Character Data in NEXUS Format

Compute Variance Component Estimates

Phylogenetic Variance-covariance or Correlation Matrix

Fits the Time-Dependent Yule Model

Fits the Yule Model With Covariates

Swapping Sister Clades

Generate Random Trees

Tree Reconstruction Based on the Triangles Method

unique.multiPhylo

Revomes Duplicate Trees

Find Patterns in DNA Sequences

Identifies Edges of a Tree

Fits the Yule Model to a Phylogenetic Tree

Write Tree File in Parenthetic Format