Eric Coissac c26623fa00 Add repeatable --exclude-genome flag to obikmer distance command ...

Integrate in-memory row/column zeroing and alignment filtering across SNP, Sankoff, TNT, and IQ-TREE output paths. Add strict validation for missing labels, implement `write_iqtree` with empirical stationary frequencies, and introduce `--raw-snp-counts` diagnostic CSV output. Update documentation to reflect experimental validation of backbone resolution limits and theoretical considerations for CTMC rate matrices.

2026-08-13 16:36:02 +02:00

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encoding.md

refactor: update core types and add approximate evidence support

2026-05-26 10:04:25 +02:00

encoding.refs.md

docs: add coverage reference files and flag architectural drift

2026-05-23 13:44:23 +02:00

entropy.md

refactor: remove equivalence class folding from entropy pipeline

2026-07-08 19:36:30 +02:00

entropy.refs.md

refactor: remove equivalence class folding from entropy pipeline

2026-07-08 19:36:30 +02:00

evolutionary_distances.md

Add repeatable --exclude-genome flag to obikmer distance command

2026-08-13 16:36:02 +02:00

indexing.md

first implementation but far to be optimal

2026-04-19 12:17:16 +02:00

indexing.refs.md

docs: add coverage reference files and flag architectural drift

2026-05-23 13:44:23 +02:00

minimizer.md

🔧 Replace degenerate minimizer logic with hash-based random ordering

2026-04-27 20:19:43 +02:00

minimizer.refs.md

docs: add coverage reference files and flag architectural drift

2026-05-23 13:44:23 +02:00