No. | **7** | | **8** |

Method | **NPRS** | | **PL** |

Author(s) | Sanderson (1997) | | Sanderson (2002) |

Software where it's implemented | r8s (Sanderson, 2003b) | treeedit (Rambaut & Charleston, 2002) | r8s (Sanderson, 2003b) |

Current version | 1.7 | 1.0a10 | 1.7 |

Runs on operating system(s) | Unix‡/Linux | Mac OS 8.6 or later, including Mac OS X | Unix‡/Linux |

Optimization strategy | Smoothing/minimizing optimality function | Smoothing/minimizing optimality function | Smoothing/minimizing optimality function |

Input data* | Phylogram (with bl) | Phylogram (with bl) | Phylogram (with bl) |

Model of rate evolution | Rate autocorrelation | Rate autocorrelation | Rate autocorrelation |

Allows multiple calibration points | Yes | No | Yes |

Accounts for multiple data sets/partitions | No | No | No |

Provides error estimates (SE/CI/CrI)† | Yes, internal and boostrap CIs | No | Yes, CI, but separate bootstrapping is required |

Accounts for phylogenetic uncertainty | No | No | No |

Ease of use | Medium | Easy (graphical user interface) | Medium |

Popularity according to literature | Popular | Popular | Becoming increasingly popular |

No. | **9** | **10** | **11** |

Method | **AHRS** | **multidivtime** | **phybayes** |

Author(s) | Yang (2004) | Thorne *et al*. (1998), Kishino *et al*. (2001) | Aris-Brosou & Yang (2002) |

Software where it is implemented | baseml (paml; Yang, 1997) | multidivtime (Thorne & Kishino, 2002) | phybayes (Aris-Brosou & Yang, 2001) |

Current version | 3.14 (since 3.14 beta 5) | 9/25/03 | 0.2e |

Runs on operating system(s) | Unix‡/Linux/Windows | Unix‡/Linux/Windows | Unix‡/Linux/Windows |

Optimization strategy | Maximum likelihood | Bayesian MCMC | Bayesian MCMC |

Input data* | Sequence data + tree topology | Sequence data + tree topology | Sequence data + tree topology |

Model of rate evolution | Rate autocorrelation | Rate autocorrelation | Rate autocorrelation |

Rates are drawn from | — | Lognormal distribution | Six different distributions |

Prior distribution of divergence time | — | Described as dirichlet distribution§ | Described as generalized birth–death process¶ |

Allows multiple calibration points | Yes | Yes, as user-specified intervals | No |

Accounts for multiple data sets/partitions | Yes | Yes | No |

Provides error estimates (SE/CI/CrI)† | Yes, CI | Yes, CrI | Yes, CrI, but must be calculated by the user |

Accounts for phylogenetic uncertainty | No | No, but accepts polytomies in input tree | No |

Ease of use | Medium | Medium (use step-by-step manual; Rutschmann, 2005) | Medium |

Popularity according to literature | Not yet very popular | Becoming increasingly popular | Not yet very popular |

No. | **12** | **13** | **14** |

Method | **Variable rate models in beast** | **Overdispersed clock** | **Compound Poisson** |

Author(s) | Drummond *et al*. (submitted) | Cutler (2000) | Huelsenbeck*et al*. (2000) |

Software where it is implemented | beast (Drummond *et al*. submitted) | c program (Cutler, 2000) | c program (Huelsenbeck*et al*., 2000) |

Current version | 1.3 | Dating5.c | —‡‡ |

Runs on operating system(s) | Unix‡/Linux/Windows, requires Java 1.4 | Unix‡/Linux/Windows | —‡‡ |

Optimization strategy | Bayesian MCMC | Maximum likelihood | Bayesian MCMC |

Input data* | Sequence data | Phylogram (with bl) | —‡‡ |

Model of rate evolution | Various models implemented** | Doubly stochastic Poisson process | Compound poisson process |

Rates are drawn from | Different distributions such as exp or lognormal | — | —‡‡ |

Prior distribution of divergence time | No specific description, priors are uniform▾ | — | —‡‡ |

Allows multiple calibration points | Yes | Yes | —‡‡ |

Accounts for multiple data sets/partitions | Yes | No | —‡‡ |

Provides error estimates (SE/CI/CrI)† | Yes, CrI | Yes, CI | —‡‡ |

Accounts for phylogenetic uncertainty | Yes | No | —‡‡ |

Ease of use | Medium, a range of tutorials is available†† | Medium | —‡‡ |

Popularity according to literature | Becoming increasingly popular | Not yet very popular | —‡‡ |