McAN

McAN constructs haplotype networks by integrating mutation spectrum history, node size, and sampling time to elucidate evolutionary relationships among closely related genomes.

Key Features:

• Mutation Spectrum History: Ensures mutations present in an ancestral haplotype are reflected in descendant haplotypes to capture mutation consistency.
• Node Size Representation: Assigns node sizes based on sample counts to represent the prevalence of specific haplotypes.
• Sampling Time Integration: Incorporates sampling time into network construction to enable temporal analysis of genome evolution.
• Performance Efficiency: Demonstrates computational efficiency reportedly two orders of magnitude faster than existing state-of-the-art algorithms while maintaining high accuracy.

Scientific Applications:

• Population genetics: Analyzes genetic diversity and haplotype relationships within populations.
• Phylogenetics: Reconstructs evolutionary relationships among closely related genomes using haplotype networks.
• Epidemiology: Tracks transmission dynamics and evolutionary changes in pathogen genomic datasets.
• SARS-CoV-2 genomic analysis: Applied to SARS-CoV-2 genomic data to study viral evolution and transmission patterns.

Methodology:

Implemented in C/C++, McAN constructs haplotype networks by ensuring ancestral-to-descendant mutation consistency, assigning node sizes from sample counts, and integrating sampling times.