mPTP

mPTP implements a multi-rate Poisson tree process to delimit species on phylogenetic trees by accounting for varying levels of intraspecific genetic variation.

Key Features:

• Phylogeny-Aware Approach: Leverages phylogenetic information to delimit species without relying on arbitrary similarity thresholds, in contrast to distance-based methods.
• Incorporation of Intraspecific Variation: Accounts for divergent intraspecific genetic variation by recognizing different levels of genetic diversity within species arising from evolutionary history or sampling strategies.
• Dynamic Programming Algorithm: Uses a novel dynamic programming algorithm to achieve a speedup of at least five orders of magnitude compared to PTP, enabling efficient processing of large (meta-) barcoding datasets.
• Markov Chain Monte Carlo (MCMC) Sampling: Employs MCMC sampling to evaluate the robustness of species delimitations, with reported evaluations completing in seconds regardless of tree size or dataset complexity.

Scientific Applications:

• Molecular Species Delimitation: Delimits species from molecular sequence data using phylogeny-aware, multi-rate models.
• Large-Scale Biodiversity and (Meta-)Barcoding Surveys: Enables rapid analysis of extensive (meta-) barcoding datasets for biodiversity assessment.
• Species Discovery and Taxonomic Assessment: Supports discovery of putative species and assessments that can be compared with established taxonomies.

Methodology:

Analyzes molecular data using a multi-rate Poisson tree process framework, implements a dynamic programming algorithm for computational acceleration, and applies Markov chain Monte Carlo (MCMC) sampling to assess delimitation support.