Change log

Major changes to OrthoSNAP are summarized here.

1.6.0 - Added batch manifest mode (–manifest) for running multiple orthogroups from one TSV/CSV. - Added input preflight and dry-run validation mode (–validate-only). - Added structured provenance outputs (–structured-output) with JSON and TSV summaries. - Added explicit occupancy semantics (–occupancy-count, –occupancy-fraction). - Added resumable execution (–resume) to skip already completed runs. - Added bootstrap consensus subgrouping (–bootstrap-trees, –consensus-min-frequency, –consensus-trees). - Improved CLI invocation handling by honoring main(argv) arguments. - Relative to 1.5.0, this release emphasizes reproducibility and workflow orchestration rather than visualization.

1.5.0 - Added -ps/–plot_snap_ogs to generate one color-coded tree figure showing inferred SNAP-OG assignments. - Added -pf/–plot_format to select png (default), pdf, or svg output for subgroup plots. - Improved runtime for duplicate-handling hotspots via faster internal indexing and pruning updates.

1.3.2 Added argument for user-defined delimiter (-d, --delimiter)

1.2.0 Added the -rih (--report_inparalog_handling) function, which creates a summary file of which inparalogs were kept compared to trimmed

0.1.0 Added -r/--rooted, -st/--snap_trees, and -ip/--inparalog_to_keep functions

1.0.0 Improved species inparalog pruning