INSANE
Insane Bayesian data augmentation
INSANE uses Bayesian data augmentation (DA) to perform inference on a number of evolutionary models on phylogenetic trees. As such, performing inference will output posterior samples for the governing parameters as well as complete or data augmented trees, that is, trees that include probable configurations of unobserved variables such as the lineages that went extinct in the past or the underlying (latent) speciation rates.
References
Constant birth-death (CBD) and birth-death diffusions (BDD): Quintero, I., Lartillot, N., Morlon, H. (2024). Imbalanced speciation pulses sustain the radiation of mammals. Science, 384: 1007-1012. link
Constant fossilized birth-death (CFBD) and fossilized birth-death diffusion (FBDD): Quintero, I., Andréoletti, J., Silvestro, D., & Morlon, H. (2025). "The rise, decline and fall of clades". BioRxiv link
Diffused Brownian motion (DBM): Quintero, I. (2025). The diffused evolutionary dynamics of morphological novelty. Proceedings of the National Academy of Sciences, U.S.A. 122 (18) e2425573122, link.