Tutorials

These task-oriented tutorials use downloadable, versioned sample data and link every workflow back to the canonical command reference.

Tutorial index

1. Summarizing information content

2. Evaluating gene-gene covariation

3. Identifying signatures of rapid radiations

4. Evaluating the accuracy of a multiple sequence alignment

5. Mapping the evolutionary history of discrete traits

6. Testing for phylogenetic signal in continuous traits

7. Phylogenetic ordination for multivariate trait analysis

8. Visualizing trait evolution with phylomorphospace

9. Phylogenetic regression (PGLS)

10. Phylogenetic GLM for binary and count data

11. Reconstructing ancestral trait values and mapping them onto a phylogeny

12. Spectral discordance decomposition

13. Testing for rate heterogeneity across phylogenetic regimes

14. Visualization commands

15. Comparing continuous trait evolution models

16. Multi-regime OU models (OUwie)

17. Automatic detection of adaptive shifts on a phylogeny

18. Visualizing conflicting phylogenetic signal with splits networks

19. End-to-end comparative methods workflow

20. Gene tree discordance analysis pipeline

21. Customizing phylogenetic plots

Legacy tutorial anchors

Tutorial 1: Summarizing information content

Tutorial 2: Evaluating gene-gene covariation

Tutorial 3: Identifying signatures of rapid radiations

Tutorial 4: Evaluating the accuracy of a multiple sequence alignment

Tutorial 5: Mapping the evolutionary history of discrete traits

Tutorial 6: Testing for phylogenetic signal in continuous traits

Tutorial 7: Phylogenetic ordination for multivariate trait analysis

Tutorial 8: Visualizing trait evolution with phylomorphospace

Tutorial 9: Phylogenetic regression (PGLS)

Tutorial 10: Phylogenetic GLM for binary and count data

Tutorial 11: Reconstructing ancestral trait values and mapping them onto a phylogeny

Tutorial 12: Spectral discordance decomposition

Tutorial 13: Testing for rate heterogeneity across phylogenetic regimes

Tutorial 14: Visualization commands

Tutorial 15: Comparing continuous trait evolution models

Tutorial 16: Multi-regime OU models (OUwie)

Tutorial 17: Automatic detection of adaptive shifts on a phylogeny

Tutorial 18: Visualizing conflicting phylogenetic signal with splits networks

Tutorial 19: End-to-end comparative methods workflow

Tutorial 20: Gene tree discordance analysis pipeline

Tutorial 21: Customizing phylogenetic plots