Add CLI subcommands to section titles + custom-proteins TSV docs - Append (prot2exon index/fetch), (prot2exon map), (prot2exon plot) to the Index/Mapping/Plotting page titles and sidebar entries. - Document the append_custom_proteins.py Input TSV, column table, and run command in Index.md, matching the current script (semicolon blocks, --in/stdout, --source-tag).
Performance: point validation/comparison links to the live proteintogenome_comparison notebook
Performance: add GenomicFeatures + VisProDom comparators (3-way 100% agreement; speed/RAM)
Restructure wiki into a sequential 7-section workflow Install -> Building an index -> Mapping -> Plotting -> Tutorials and notebooks -> Performance and benchmarking -> Reference. Merge the old scattered pages (Genome-onboarding + Custom-proteins -> Index; Output-modes + Input-format -> Mapping; Performance-and-RAM + Validation + Benchmarks -> Performance and benchmarking); drop the standalone Quickstart and CLI-reference. Update all CLI to the four-command form (index / map / fetch / plot) and the fetch-defaults-to-Zenodo model. Sidebar lists each section's subsections.
Initial wiki — 17 pages mirrored from main repo wiki/
Initial Home page