Abstract
<jats:p>Coordinate-based exclusion of genomic regions is routine in microbial phylogenomics, yet the editing step often relies on ad hoc scripts or manual alignment manipulation. This simple but high-consequence task can alter the character matrix, retain unwanted signal, or leave invalid NEXUS dimensions. This study presents NEXCISION, a dependency-free Python command-line tool for exact removal of coordinate-labelled rows from transposed NEXUS matrices. NEXCISION uses 1-based inclusive intervals, preserves retained rows and surrounding NEXUS content, updates matrix dimensions, reports interval-specific removal counts, and can generate deterministic provenance reports with SHA-256 checksums. Correctness was evaluated using three genuine SPANDx-derived matrices, an independent oracle, 17 correctness and preservation cases, 26 malformed-input challenges, 1,000 synthetic matrices containing 304,000 site rows, nine property-based invariants across 1,800 examples, and 12 deliberately faulted implementations. All expected rows were removed, retained rows and state strings were preserved, malformed inputs failed safely, and all deliberate faults were detected. In 105 measured scalability runs, NEXCISION remained correct and deterministic across 21 configurations. Runtime scaled near-linearly from ~100 MB to 5 GB, processing a 4.83 GiB matrix in ~24.2 seconds on one pinned logical central processing unit. Up to 100,000 intervals added modest runtime, while peak memory increased by ~4.85 GiB per GiB of input. NEXCISION makes a fragile bespoke editing step exact, testable, and provenance-rich for microbial phylogenomics.</jats:p>