The following pages and posts are tagged with

TitleTypeExcerpt
Adaptive MCMC Tutorial Page Using adaptive MCMC to update continuous parameters in BEAST.
Effective Sample Size (ESS) Page About the Effective Sample Size (ESS) and how to increase it.
Optimizing Performance Page Optimizing Performance
Continuous Phylogeography Tutorial Page
Analysing Continuous Traits Page How to jointly estimate a molecular phylogenetic tree and 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 ...
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.
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...
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...
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.
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 ...
Phylogeographic Diffusion in Continuous Space 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 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...
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...