- Generate PyRate input file (option 1)
- Generate PyRate input file (option 2)
- Check species list for inconsistent spelling and typos
- Setting up a preservation model
- Birth-death with rate shifts using RJMCMC (recommended algorithm)
- Birth-death with rate shifts using BDMCMC
- Birth-death models with fixed times bins
- Running PyRate on large datasets
- Plotting marginal rates (RJMCMC)
- Plotting and summarizing BDMCMC output
- Plotting preservation rates through time
- Plotting range-through diversity trajectories
- Generating input file for PyRateContinuous
- Diversity dependent birth-death models
- Correlation with a time-continuous variable
- Model testing using marginal likelihoods
- Multiple-clade diversity dependent model
- Multivariate birth-death model (multiple time-continuous correlates)
- Trait dependent birth-death models
- Age dependent extinction model
- Birth-death Chronospecies model
- Birth-death neural network (BDNN) model