MP3tree

MP3tree computes MP3 (Multi-Phenotype Phylogenetic Similarity), a triplet-based similarity measure to compare fully multi-labeled tumor phylogenetic trees with poly-occurring labels and to classify tumor evolutionary histories that include simultaneous and repeated mutations.

Key Features:

• Handling Poly-Occurring Mutations: Manages poly-occurring labels in fully multi-labeled tumor phylogenies, including simultaneous and repeated mutation events.
• Robust Similarity Measure: Implements MP3 as a triplet-based similarity score to evaluate and classify trees as similar or dissimilar.
• Validation on Data: Demonstrated on both simulated and real datasets to assess performance on practical cancer phylogeny scenarios.

Scientific Applications:

• Comparison of Tumor Phylogenies: Enables evaluation and comparison of alternative inferred evolutionary histories of tumors.
• Accommodation of Complex Mutation Patterns: Improves phylogenetic analyses by accounting for simultaneous and repeated mutations in tumor evolution.
• Support for Precision Oncology: Provides phylogenetic insights that can inform development of personalized cancer treatment strategies.

Methodology:

Computes a triplet-based similarity score (MP3) that explicitly accounts for poly-occurring labels in fully multi-labeled trees and for simultaneous and repeated mutations.