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A comprehensive list of phylogenetics packages for R

The packages
Here is my comprehensive list of phylogenetics packages for R, with links to their websites (for some, links to support pages or more detailed information are provided in subsequent sections).  The requirement for inclusion in the list is at least one function related to manipulation or analysis of phylogenetic data.  Please E-mail me if you know of another program to add, or if you are developing a new package for phylogenetics in R.  The packages, listed in alphabetical order, are as follows:** **

  1. ade4, Analysis of Ecological Data: Exploratory and Euclidian methods in Environmental sciences (link)
  2. ape, Analysis of Phylogenetics and Evolution (link)
  3. apTreeshape, Analyses of Phylogenetic Treeshape (link)
  4. auteur (no longer supported but available from archive, see other; link)
  5. BioGeoBEARS,  BioGeography with Bayesian (and likelihood) Evolutionary Analysis in R Scripts (link; and accessory packages:)
  6. caper, Comparative Analyses of Phylogenetics and Evolution in R (link)
  7. cladoRcpp (link)
  8. distory, Distance Between Phylogenetic Histories (link)
  9. diversitree, diversitree: comparative phylogenetic analyses of diversification (link)
  10. geiger, analysis of evolutionary diversification (link)
  11. geomorph, Geometric Morphometric analyses of 2d/3d landmark data (link)
  12. HMPTrees, Statistical Object Oriented Data Analysis of RDP-based Taxonomic trees from Human Microbiome Data: Modeling, Visualization, and Two-Group Comparison
  13. LAGOPUS, LAGOPUS: Bayesian relaxed clock dating with the multidivtime method (link)
  14. laser, Likelihood Analysis of Speciation/Extinction Rates from phylogenies (link)
  15. MCMCglmm, MCMC Generalized Linear Mixed Models (link)
  16. metafor, Meta-Analysis Package for R (link)
  17. nlme, Linear and Nonlinear Mixed Effect Models (link)
  18. OUCH, Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses (link)
  19. OUwie, Analysis of evolutionary rates in an OU framework (link)
  20. paleotree, Paleontological and Phylogenetic Analyses of Evolution (link)
  21. phangorn, Phylogenetic analysis in R (link)
  22. phyclust, Phylogenetic Clustering (phyloclustering) (link)
  23. phylobase, Base package for phylogenetic structures and comparative data (link)
  24. phyloch, PHYLOCH: interfaces and graphic tools for phylogenetic data in R (link)
  25. phyloclim, PHYLOCLIM: phyloclimatic modeling in R (link)
  26. phylocom, Software for the Analysis of Phylogenetic Community Structure and Character Evolution, with Phylomatic (link)
  27. phylogr (no longer supported but available from archive, see other; link)
  28. phylolm, Phylogenetic Linear Regression (link)
  29. phylosim, R package for simulation biological sequence evolution (link)
  30. phytools, Phylogenetic Tools for comparative biology (and other things) (link)
  31. picante, R tools for integrating phylogenies and ecology (link)
  32. pmc (no longer supported but available from archive, see other; link)
  33. PVR, Computes phylogenetic eigenvectors regression (PVR) and phylogenetic signal representation curve (PSR) (with null and Brownian expectations) (link)
  34. qpcR, Modelling and analysis of real-time PCR data (link)
  35. rexpokit (link)
  36. rmesquite (link; also see companion package, Mesquite.R)
  37. scaleboot, Approximately Unbiased P-values via Multiscale Bootstrap (link)
  38. spider, Species Identity and Evolution in R (link)
  39. SymmeTREE, whole-tree analysis of differential diversification rates (link)
  40. SYNCSA, Analysis of functional and phylogenetic patterns in metacommunities (link)
  41. TESS, Fast simulation of reconstructed phylogenetic trees under time-dependent birth-death processes (link)
  42. treebase, An R package for discovery, access and manipulation of online phylogenies (link)
  43. TreeSim, Simulating trees under the birth-death model (link)
  44. vegan, Community Ecology Package (link)

Broad overview: a brief summary of what the packages do

[More coming soon.]