MODIFI detects DNA base modifications and infers host-mobile genetic element (MGE) linkages from PacBio metagenomic sequencing data. It supports modification calling, motif discovery, and host-MGE association for both subreads and HiFi read types. Native motif finding uses pbmotifmaker (from pbtk) on Linux if installed; otherwise use the bundled MultiMotifMaker.jar (OpenJDK). On macOS, install PacBio tools separately or rely on the JAR fallback.