Introduction | fasta_filename | inference_model and mcmc | site_model | clock_model | tree_prior | mrca_prior

Introduction | Create a 'BEAST2' input file | Display (part of) the 'BEAST2' input file | Run MCMC | Display (part of) the 'BEAST2' output files | Parse output

Introduction | Setup | Experiment | Do the run | References

Introduction | Getting started | Method

Introduction | Let babette run 'BEAST2' | Plot the posterior estimates | Show the effective sample sizes (ESS) | Show the summary statistics | Plot the posterior phylogenies

Introduction | Example #1: all default | Example #2: using an MRCA prior to specify a crown age | Example #3: JC69 site model | Example #4: Relaxed clock log normal | Example #5: Birth-Death tree prior | Example #6: Yule tree prior with a normally distributed birth rate | Example #7: HKY site model with a non-zero proportion of invariants | Example #8: Strict clock with a known clock rate

Introduction

Introduction | Demonstration | Cleanup

Introduction | Getting started | Example #1: all default | Example #2: JC69 site model | Example #3: Relaxed clock log normal | Example #4: Birth-Death tree prior | Example #5: Yule tree prior with a normally distributed birth rate | Example #6: HKY site model with a non-zero proportion of invariants | Example #7: Strict clock with a known clock rate | Example #8: Use MRCA prior | Example #9: Use MRCA prior to specify a close-to-fixed crown age | Cleanup

Introduction | Getting started | Default inference model | Site models | Clock models | Tree prior | (optional) MRCA prior: a 'Most Recent Common Ancestor' | MCMC: the Markov Chain Monte Carlo setup | (optional) BEAUti options: version-specific options | (experimental) a tipdates filename: a filename for tip-dating

Appendix | All example files | All MHC-I haplotypes | All MHC-II haplotypes | Session info

Introduction | List all BEAST2 packages | Install the first non-installed BEAST2 package | Uninstall the BEAST2 package