NEXCISION

NEXCISION enables exact, validated excision of coordinate-defined genomic regions from transposed NEXUS matrices.

Key Features:

• Coordinate-based row removal: Uses 1-based inclusive intervals to remove coordinate-labelled rows from transposed NEXUS matrices.
• Content preservation: Preserves retained rows, surrounding NEXUS content, and state strings during excision.
• Matrix integrity maintenance: Updates NEXUS matrix dimensions automatically after row removal.
• Removal reporting: Reports interval-specific removal counts for each excision operation.
• Provenance tracking: Generates deterministic provenance reports with SHA-256 checksums.
• Failure safety: Handles malformed inputs safely without corrupting output.
• Scalability: Processes matrices from approximately 100 MB to 5 GB with near-linear runtime scaling.

Scientific Applications:

• Microbial phylogenomics: Replaces ad hoc scripts and manual alignment manipulation for coordinate-based exclusion of genomic regions in phylogenetic analyses.
• Microbial genomic epidemiology: Supports trustworthy removal of defined regions prior to downstream phylogenetic inference.
• Outbreak analysis: Enables precise excision of reference-defined sites from transposed NEXUS matrices in pathogen tracking workflows.
• Recombination masking: Facilitates removal of recombinant genomic regions identified by detection tools.
• Mobile-element studies: Supports excision of mobile genetic elements from phylogenomic matrices.

Methodology:

NEXCISION is implemented as a dependency-free Python command-line tool (Python >=3.10) that operates as a single-process utility. Correctness was evaluated using three 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.