adephylo:
exploratory analyses for the phylogenetic comparative method

ape:
Analyses of Phylogenetics and Evolution

apTreeshape:
Analyses of Phylogenetic Treeshape

BAMMtools:
Analysis and visualization of macroevolutionary dynamics on phylogenetic trees

caper:
Comparative Analyses of Phylogenetics and Evolution in R

cladoRcpp:
C++ implementations of phylogenetic calculations

corHMM:
Analysis of binary character evolution

DDD:
Diversity-dependent diversification

distory:
Distance Between Phylogenetic Histories

diversitree:
comparative phylogenetic analyses of diversification

evobiR:
evolutionary biology in R

expoTree:
Calculate density dependent likelihood of a phylogenetic tree

geomorph:
Geometric morphometric analyses of 2d/3d landmark data

GUniFrac:
Generalized UniFrac distances

HMPTrees:
Statistical Object Oriented Data Analysis of RDP-based Taxonomic trees from Human Microbiome Data
Modeling, Visualization, and Two-Group Comparison

HyPhy:
Macroevolutionary phylogentic analysis of species trees and gene trees

iteRates:
Parametric rate comparison

laser:
Likelihood Analysis of Speciation/Extinction Rates from Phylogenies

MPSEM:
Modeling Phylogenetic Signals using Eigenvector Maps

mvSLOUCH:
MultiVariate Stochastic Linear Ornstein-Uhlenbeck models for phylogenetic Comparative hypotHeses

ouch:
Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses

paleotree:
Paleontological and Phylogenetic Analyses of Evolution

pastis:
Phylogenetic Assembly with Soft Taxonomic Inferences

PCPS:
PCPS - Principal Coordinates of Phylogenetic Structure

pGLS:
Generalized Least Square in comparative Phylogenetics

phangorn:
Phylogenetic analysis in R

phyclust:
Phylogenetic Clustering (Phyloclustering)

phyext:
An extension of some of the classes in phylobase. Tree objects now support subnodes on branches

phylobase:
Base package for phylogenetic structures and comparative data

phyloclim:
Integrating Phylogenetics and Climatic Niche Modeling

phyloland:
Modelling Competitive Exclusion and Limited Dispersal in a Statistical Phylogeographic Framework

phylolm:
Phylogenetic Linear Regression

phylotools:
Phylogenetic tools for Eco-phylogenetics

phyreg:
Implements the Phylogenetic Regression of Grafen (1989)

phytools:
Phylogenetic Tools for comparative biology (and other things)

picante:
R tools for integrating phylogenies and ecology

PVR:
Computes phylogenetic eigenvectors regression (PVR) and phylogenetic signal-representation curve (PSR) (with null and Brownian expectations)

RADami:
R Package for Phylogenetic Analysis of RADseq Data

SigTree:
Determine significantly responsive branches in phylogenetic trees

spacodiR:
Spatial and Phylogenetic Analysis of Community Diversity

spider:
Species Identity and Evolution in R

SYNCSA:
Analysis of functional and phylogenetic patterns in metacommunities

TESS:
Fast simulation of reconstructed phylogenetic trees under time-dependent birth-death processes

treebase:
An R package for discovery, access and manipulation of online phylogenies

TreePar:
Estimating birth and death rates based on phylogenies

TreeSimGM:
Simulating Phylogenetic Trees under a General Model