FGTpartitioner

FGTpartitioner partitions large genome-wide single nucleotide polymorphism (SNP) datasets into ancestry blocks to delimit ancestry breakpoints for phylogenomic and evolutionary analyses.

Key Features:

• Efficiency: Processes full-chromosome alignments significantly faster than existing solutions, achieving orders of magnitude improvements in runtime.
• No Phasing Requirement: Operates on unphased data without haplotype phasing, enabling analysis of diploid and non-model organisms where phasing is challenging or intractable.
• Parallelization: Leverages native parallelization techniques to increase computational throughput for large genome-wide SNP datasets.

Scientific Applications:

• Phylogenomic inference: Delimits ancestry breakpoints across genomes to support phylogenomic analyses of evolutionary relationships.
• Genetic diversity and population structure: Provides rapid delimitation of ancestry blocks to inform studies of genetic diversity, population structure, and evolutionary history.
• Large and non-model genomes: Applies to large, whole-chromosome SNP alignments and non-model diploid organisms where phasing is intractable.

Methodology:

Implements algorithmic improvements to partition genome alignments into ancestry blocks without requiring pre-phased haplotypes and uses native parallelization to process full-chromosome alignments efficiently.