#35 · Genomics

Combinatorial path and block alignment formalized for pangenomes, genealogies, synteny

The dominant thread is combinatorial alignment of ordered sequence elements to structured reference objects, with each formulation defined by explicit path or block constraints. The pangenome preprint enumerates all maximal graph paths matching a given sequence chain under user-specified maximal gaps, the only item that performs direct sequence-to-graph alignment. The gene-tree preprint enumerates consistent ancestry paths linking genetic trees to genealogical pedigrees, demonstrated on the BALSAC Quebec dataset. The synteny preprint derives blocks from sequence elements without breakpoints, establishing NP-hard problems and a linear-time algorithm for collinear blocks. What is new is the explicit combinatorial formalization of these targets rather than general-purpose indexing primitives. The summaries report no benchmarks, so performance remains unverified.