Phylogenetics - CRAN Task View

adephylo

Exploratory Analyses for the Phylogenetic Comparative Method

Version 1.1-16

adiv

Analysis of Diversity

Version 2.2.1

ape

Analyses of Phylogenetics and Evolution

Version 5.8

apex

Phylogenetic Methods for Multiple Gene Data

Version 1.0.6

aphid

Analysis with Profile Hidden Markov Models

Version 1.3.5

aphylo

Statistical Inference and Prediction of Annotations in Phylogenetic Tr...

Version 0.3-3

ips

Interfaces to Phylogenetic Software in R

Version 0.0.12

evobiR

Comparative and Population Genetic Analyses

Version 1.1

DDD

Diversity-Dependent Diversification

Version 5.2.2

beautier

'BEAUti' from R

Version 2.6.12

betapart

Partitioning Beta Diversity into Turnover and Nestedness Components

Version 1.6

BoSSA

A Bunch of Structure and Sequence Analysis

Version 3.7

caper

Comparative Analyses of Phylogenetics and Evolution in R

Version 1.0.3

GUniFrac

Generalized UniFrac Distances, Distance-Based Multivariate Methods and...

Version 1.8

EvoPhylo

Pre- And Postprocessing of Morphological Data from Relaxed Clock Bayes...

Version 0.3.2

DAMOCLES

Dynamic Assembly Model of Colonization, Local Extinction and Speciatio...

Version 2.3

HMPTrees

Statistical Object Oriented Data Analysis of RDP-Based Taxonomic Trees...

Version 1.4

dendextend

Extending 'dendrogram' Functionality in R

Version 1.17.1

dispRity

Measuring Disparity

Version 1.8

distory

Distance Between Phylogenetic Histories

Version 1.4.4

geiger

Analysis of Evolutionary Diversification

Version 2.0.11

BAMMtools

Analysis and Visualization of Macroevolutionary Dynamics on Phylogenet...

Version 2.1.12

ggmuller

Create Muller Plots of Evolutionary Dynamics

Version 0.5.6

epm

EcoPhyloMapper

Version 1.1.3

hisse

Hidden State Speciation and Extinction

Version 2.1.11

idendr0

Interactive Dendrograms

Version 1.5.3

markophylo

Markov Chain Models for Phylogenetic Trees

Version 1.0.9

motmot

Models of Trait Macroevolution on Trees

Version 2.1.3

nLTT

Calculate the NLTT Statistic

Version 1.4.9

ouch

Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses

Version 2.20

PBD

Protracted Birth-Death Model of Diversification

Version 1.4

PCPS

Principal Coordinates of Phylogenetic Structure

Version 1.0.7

phyclust

Phylogenetic Clustering (Phyloclustering)

Version 0.1-34

phyext2

An Extension (for Package 'SigTree') of Some of the Classes in Package...

Version 0.0.4

phylocanvas

Interactive Phylogenetic Trees Using the 'Phylocanvas' JavaScript Libr...

Version 0.1.3

phyloclim

Integrating Phylogenetics and Climatic Niche Modeling

Version 0.9.5

PHYLOGR

Functions for Phylogenetically Based Statistical Analyses

Version 1.0.11

phylogram

Dendrograms for Evolutionary Analysis

Version 2.1.0

phyloregion

Biogeographic Regionalization and Macroecology

Version 1.0.8

phylotate

Phylogenies with Annotations

Version 1.3

phylotools

Phylogenetic Tools for Eco-Phylogenetics

Version 0.2.2

phyreg

The Phylogenetic Regression of Grafen (1989)

Version 1.0.2

picante

Integrating Phylogenies and Ecology

Version 1.8.2

pmc

Phylogenetic Monte Carlo

Version 1.0.6

secsse

Several Examined and Concealed States-Dependent Speciation and Extinct...

Version 3.1.0

windex

Analysing Convergent Evolution using the Wheatsheaf Index

Version 2.0.8

RPANDA

Phylogenetic ANalyses of DiversificAtion

Version 2.3

treebase

Discovery, Access and Manipulation of 'TreeBASE' Phylogenies

Version 0.1.5

Rphylopars

Phylogenetic Comparative Tools for Missing Data and Within-Species Var...

Version 0.3.10

treebalance

Computation of Tree (Im)Balance Indices

Version 1.2.0

tidytree

A Tidy Tool for Phylogenetic Tree Data Manipulation

Version 0.4.6

RevGadgets

Visualization and Post-Processing of 'RevBayes' Analyses

Version 1.2.1

Rogue

Identify Rogue Taxa in Sets of Phylogenetic Trees

Version 2.1.6

phangorn

Phylogenetic Reconstruction and Analysis

Version 2.12.1

tracerer

Tracer from R

Version 2.2.3

RNeXML

Semantically Rich I/O for the 'NeXML' Format

Version 2.4.11

rncl

An Interface to the Nexus Class Library

Version 0.8.7

TESS

Diversification Rate Estimation and Fast Simulation of Reconstructed P...

Version 2.1.2

Revticulate

Interaction with "RevBayes" in R

Version 1.0.0

phylobase

Base Package for Phylogenetic Structures and Comparative Data

Version 0.8.12

TBRDist

Rearrangement Distances Between Unrooted Phylogenetic Trees

Version 1.0.2

treedater

Fast Molecular Clock Dating of Phylogenetic Trees with Rate Variation

Version 0.5.0

SYNCSA

Analysis of Functional and Phylogenetic Patterns in Metacommunities

Version 1.3.4

TreeSim

Simulating Phylogenetic Trees

Version 2.4

SigTree

Identify and Visualize Significantly Responsive Branches in a Phylogen...

Version 1.10.6

ggplot2

Create Elegant Data Visualisations Using the Grammar of Graphics

Version 3.5.1

CRABS

Congruent Rate Analyses in Birth-Death Scenarios

Version 1.2.0

Quartet

Comparison of Phylogenetic Trees Using Quartet and Split Measures

Version 1.2.6

phylosignal

Exploring the Phylogenetic Signal in Continuous Traits

Version 1.3.1

treespace

Statistical Exploration of Landscapes of Phylogenetic Trees

Version 1.1.4.3

rotl

Interface to the 'Open Tree of Life' API

Version 3.1.0

phyloTop

Calculating Topological Properties of Phylogenies

Version 2.1.2

paleobuddy

Simulating Diversification Dynamics

Version 1.0.0

FossilSim

Simulation and Plots for Fossil and Taxonomy Data

Version 2.4.1

metafor

Meta-Analysis Package for R

Version 4.6-0

brms

Bayesian Regression Models using 'Stan'

Version 2.22.0

OUwie

Analysis of Evolutionary Rates in an OU Framework

Version 2.10

MPSEM

Modelling Phylogenetic Signals using Eigenvector Maps

Version 0.4-4

phytools

Phylogenetic Tools for Comparative Biology (and Other Things)

Version 2.3-0

TreeTools

Create, Modify and Analyse Phylogenetic Trees

Version 1.12.0

paleoTS

Analyze Paleontological Time-Series

Version 0.6.2

beastier

Call 'BEAST2'

Version 2.5.1

TreeSearch

Phylogenetic Analysis with Discrete Character Data

Version 1.5.1

MCMCglmm

MCMC Generalised Linear Mixed Models

Version 2.36

strap

Stratigraphic Tree Analysis for Palaeontology

Version 1.6-1

geomorph

Geometric Morphometric Analyses of 2D and 3D Landmark Data

Version 4.0.8

RRPP

Linear Model Evaluation with Randomized Residuals in a Permutation Pro...

Version 2.0.3

babette

Control 'BEAST2'

Version 2.3.4

phylolm

Phylogenetic Linear Regression

Version 2.6.5

diversitree

Comparative 'Phylogenetic' Analyses of Diversification

Version 0.10-1

castor

Efficient Phylogenetics on Large Trees

Version 1.8.2

tbea

Pre- And Post-Processing in Bayesian Evolutionary Analyses

Version 1.5.0

mvMORPH

Multivariate Comparative Tools for Fitting Evolutionary Models to Morp...

Version 1.2.1

paleotree

Paleontological and Phylogenetic Analyses of Evolution

Version 3.4.7

treestats

Phylogenetic Tree Statistics

Version 1.70.5

convevol

Analysis of Convergent Evolution

Version 2.2.1

deeptime

Plotting Tools for Anyone Working in Deep Time

Version 2.0.0

surface

Fitting Hansen Models to Investigate Convergent Evolution

Version 0.6

taxize

Taxonomic Information from Around the Web

Version 0.9.100.1

entropart

Entropy Partitioning to Measure Diversity

Version 1.6-15

vegan

Community Ecology Package

Version 2.6-8

Claddis

Measuring Morphological Diversity and Evolutionary Tempo

Version 0.7.0

TreeDist

Calculate and Map Distances Between Phylogenetic Trees

Version 2.9.1

CALANGO

Comparative Analysis with Annotation-Based Genomic Components

Version 1.0.20