Issues

• Set an upper bound on taxa for the pairwise pipeline (cost model)

  stajichlab/NovInvenio#220 · Filter by author hyphaltip opened on Oct 8, 2026

• Deprecate and remove the mmseqs and novelty_discovery --cluster_tool pathways

  stajichlab/NovInvenio#219 · Filter by author hyphaltip opened on Oct 8, 2026

• Record other-group evidence (incl. paralog E-value) and add a coverage-based outgroup signal class to novelty tables and pages

  stajichlab/NovInvenio#208 · Filter by author hyphaltip opened on Sep 28, 2026

• famsa -t N is ~900x slower than -t 1 on AVX2 nodes under sbatch (affects BUILD_CHUNK)

  stajichlab/NovInvenio#181 · Filter by author hyphaltip opened on Sep 24, 2026

• Carry alignment coverage for phmmer hits (needs --domtblout, not a wider --tblout)

  stajichlab/NovInvenio#150 · Filter by author hyphaltip opened on Sep 21, 2026

• Ship a dispatch-correct famsa build so BUILD_CHUNK is not pinned to AVX2 nodes

  stajichlab/NovInvenio#148 · Filter by author hyphaltip opened on Sep 21, 2026

• pangenome: sensitivity analysis of unvalidated cutoffs, starting with tier1_min_id

  stajichlab/NovInvenio#132 · Filter by author hyphaltip opened on Sep 20, 2026
  4