FBD Parameters Statistics and Plots (Mr. Bayes) | 1. Import combined log file from all runs. | 2. Summarize FBD parameters by time bin | 3. Plot the distribution of each FBD parameter | 4. Test for assumptions | 5. Test for significant FBD shifts between time bins | FBD Parameters Statistics and Plots (BEAST2) | References

Analyzing Trees With Offset ages (BEAST2) | 1. Import the posterior tree distribution. | 2. Summarize the modified tree distribution | 3. Restore the final summary tree | Analyzing Trees With Offset ages (Mr.Bayes) | References

Character Partitioning (Case 1) | 1. Generate distance matrix | 2. Estimate the optimal number of partitions | 3. Simple Workflow | 4. Complete Workflow | Character Partitioning (Case 2) | 3. Complete Workflow | References

Evolutionary Rates Statistics and Plots | 0. Set your BEAST2 analysis to log multiple clocks | 1. Get rates from the clock tree and create a rate table | 2. Export the rate table and plot tree with node values | Plot tree node labels to customize clade names | 3. Import rate table with custom clade memberships | 4. Get summary stats for each clade/clock partition | 5. Plot rates by clock partition and clade | 6. Rate linear models | Selection Mode | 1. Import posterior log file | 3. Plot selection gradient on the summary tree | 4. Pairwise t-tests of rate values among clades | References

Evolutionary Rates Statistics and Plots | 1. Get rates from the clock tree and create a rate table | 2. Export the rate table and plot tree with node values | Plot tree node labels to customize clade names | 3. Import rate table with custom clade memberships | 4. Get summary stats for each clade/clock partition | 5. Plot rates by clock partition and clade | 6. Rate linear models | ADDENDUM: Example using rates from single clock analysis (no partitioning) | Selection Mode | 1. Import combined log file from all runs. | 3. Plot selection gradient on the summary tree | 4. Pairwise t-tests of rate values among clades | References

Creating Inter-character Distance Matrices | Types of morphological data | Treatment of inapplicable and missing data