ConTreeDP

ConTreeDP constructs consensus clonal phylogenetic trees from heterogeneous cancer genomic data to infer tumor evolutionary history.

Key Features:

• Maximum Directed Partition Support Consensus Tree (MDPSCT) Formulation: Implements the MDPSCT formulation to compute consensus trees for clonal phylogenetics.
• Efficiency and Accuracy: Provides a method that has been validated theoretically and empirically to compute clonal consensus trees with high efficiency and accuracy.
• Handling Heterogeneous Data: Integrates heterogeneous cancer genomic data arising from diverse somatic mutability mechanisms into consensus phylogenies.
• Short Evolutionary Timescales: Accounts for rapid mutation rates and short evolutionary timescales typical of tumor progression.

Scientific Applications:

• Tumor evolutionary history inference: Reconstructs tumor evolutionary histories from clonal genomic data.
• Subclonal population identification: Supports identification and characterization of subclonal populations within tumor samples.
• Elucidation of tumorigenesis mechanisms: Aids in resolving clonal relationships to investigate mechanisms driving tumorigenesis.

Methodology:

Solves the Maximum Directed Partition Support Consensus Tree (MDPSCT) problem to derive consensus clonal phylogenies and integrates diverse cancer genomic data; the algorithm has been validated both theoretically and empirically.