The following pages and posts are tagged with

Title | Type | Excerpt |
---|---|---|

Adaptive MCMC Tutorial | Page | Using adaptive MCMC to update continuous parameters in BEAST. |

Optimizing Performance | Page | Optimizing Performance |

Using BETS to evaluate temporal signal | Page | This tutorial describes the use of BETS (Bayesian Evaluation of Temporal Signal) to examine the temporal signal of a data set. |

Continuous Phylogeography Tutorial | Page | |

Analysing Continuous Traits | Page | How to jointly estimate a molecular phylogenetic tree and the coevolutionary patterns of morphological traits. |

Analysing Continuous Traits without Sequence Data | Page | How to estimate the coevolutionary patterns of morphological traits. |

Discrete Phylogeography Tutorial | Page | |

Discrete Trait Tutorial | Page | |

Epoch Model Tutorial | Page | Setting up time-heterogeneous epoch substitution models in BEAST. |

First Tutorial | Page | An introductory tutorial to getting started with BEAST. This tutorial describes the use of BEAUti and BEAST to analyse some primate sequences and estimate a ... |

How to setup hierarchical models for sets of parameters | Page | Setting up hierarchical phylogenetic models for different scenarios. |

Markov Jumps and Rewards | Page | Obtaining Markov jump counts and Markov rewards. |

Markov Jumps and Rewards | Page | A process of discrete state transitioning in evolutionary history is generally modelled using a continuous-time Markov chain (CTMC) model. This is the case f... |

Markov-modulated Models Tutorial | Page | Constructing Markov-modulated substitution model XML files for use with BEAST. |

Model Averaging for Clocks Tutorial | Page | Bayesian model averaging (BMA) for relaxed clocks in BEAST. |

Model Selection Tutorial | Page | Model selection using path sampling / stepping-stone sampling in BEAST. |

Model Selection Advanced Tutorial | Page | Model selection using generalized stepping-stone sampling in BEAST. |

Online Bayesian Phylodynamic Inference Tutorial | Page | Using online Bayesian phylodynamic inference to add sequences to an ongoing analysis in BEAST. |

The evolutionary dynamics of a influenza epidemic | Page | This tutorial provides a step-by-step explanation on how to reconstruct the evolutionary dynamics of influenza based on a set of virus sequences which have b... |

Revealing the fluctuating evolutionary dynamics of seasonal influenza | Page | This tutorial provides a step-by-step explanation on how to reconstruct the evolutionary dynamics of seasonal influenza based on a set of H3N2 virus sequence... |

Estimating rates and dates from time-stamped sequences | Page | This chapter provides a step-by-step tutorial for analyzing a set of virus sequences which have been isolated at different points in time (heterochronous dat... |

Second Tutorial | Page | This is the second introductory tutorial to BEAST. Here we will continue the analysis from the first tutorial looking at the output, diagnosing problems and ... |

Sequential Monte Carlo BEAST Tutorial | Page | Using Sequential Monte Carlo to add sequences to an ongoing analysis in BEAST. |

Using TempEst for data exploration | Page | This tutorial describes the use of TempEst to examine the temporal signal of a data set and to look for problematic or erroneous sequences. |

Approaches for analyzing large phylogenetic datasets | Page | This tutorial offers a summary of approaches that can be used to more efficiently analyze large datasets with an emphasis on methods targeted at SARS-CoV-2. |

Time Dependent Rates | Page | Setting up a time-dependent rate (TDR) model in BEAST. |

Accommodating individual travel history in discrete phylogeographic diffusion | Page | This tutorial provides a step-by-step explanation on accommodating/including the travel history of multiple individuals into discrete phylogeographic analysis. |

Phylogeographic Diffusion in Continuous Space - WNV example | Page | This tutorial provides a step-by-step explanation on reconstructing the spatial dynamics of the West Nile virus (WNV) invasion across North America based on ... |

Phylogeographic Diffusion in Continuous Space - YFV example | Page | This tutorial provides a step-by-step explanation on reconstructing the spatial dynamics of the Yellow fever virus (YFV) epidemic in Brazil based on a set of... |

Phylogeographic diffusion in discrete space | Page | This chapter provides a step-by-step tutorial on reconstructing the spatial dispersal and cross-species dynamics of rabies virus (RABV) in North American bat... |

Visualizing phylogenetic trees using FigTree | Page | This tutorial provides a step-by-step tutorial for analyzing an Ebola virus timetree. This tutorial can be easily adapted to display and summarize annotated ... |

Practical genomic epidemiology | Page | This tutorial presents an outbreak scenario that starts with a small number of initial cases with no known infectious agent. We will initially identify the p... |

Revealing the evolutionary dynamics of influenza | Page | This tutorial provides a step-by-step explanation on how to reconstruct the evolutionary dynamics of influenza based on a set of virus sequences which have b... |

Model Selection and Testing | Page | This tutorial continues the analysis of yellow fever virus (YFV) from the Estimating rates and dates from time-stamped sequences tutorial. Here we use margin... |

Estimating rates and dates from time-stamped sequences | Page | This tutorial provides a step-by-step tutorial for analyzing a set of virus sequences which have been isolated at different points in time (heterochronous da... |

Phylodynamic inference of respiratory viruses | Page | This tutorial provides a step-by-step explanation on how to reconstruct the evolutionary dynamics of respiratory viruses based on sets of virus sequences tha... |