Issues

• Root-level groups that start with a duplication can get a TaxRange that is too old

  DessimozLab/FastOMA#128 · Filter by author alpae opened on Nov 5, 2026

• Tracking: bugs found by the test suite ahead of the ete4 migration

  bug
  DessimozLab/FastOMA#124 · Filter by author alpae opened on Nov 4, 2026

• Report fails when CompletenessScore is disabled

  bug
  DessimozLab/FastOMA#123 · Filter by author alpae opened on Nov 4, 2026

• Small internal bugs in HOG class, UnionFind, batching and orthoXML helpers

  bug
  DessimozLab/FastOMA#122 · Filter by author alpae opened on Nov 4, 2026

• Bring fragment handling back to life (--overlap-fragments has no effect)

  enhancement
  DessimozLab/FastOMA#121 · Filter by author alpae opened on Nov 4, 2026

• Discussion: future of the gene tree rooting methods (mad, Nevers_rooting, outlier)

  discussion
  DessimozLab/FastOMA#120 · Filter by author alpae opened on Nov 4, 2026

• Output depends on PYTHONHASHSEED and on Nextflow task completion order

  bug
  DessimozLab/FastOMA#119 · Filter by author alpae opened on Nov 4, 2026

• Input validation: crashes and misleading errors in check-input and infer-roothogs

  bug
  DessimozLab/FastOMA#118 · Filter by author alpae opened on Nov 4, 2026

• Species-overlap reconciliation mislabels duplications at gene-tree polytomies

  bug
  DessimozLab/FastOMA#117 · Filter by author alpae opened on Nov 4, 2026

• Output orthoXML violates the OrthoXML 0.5 schema

  bug
  DessimozLab/FastOMA#116 · Filter by author alpae opened on Nov 4, 2026

• ImpliedLosses score is wrong: species tree nodes are compared by identity

  bug
  DessimozLab/FastOMA#115 · Filter by author alpae opened on Nov 4, 2026

• infer-roothogs silently drops proteins

  bug
  DessimozLab/FastOMA#114 · Filter by author alpae opened on Nov 4, 2026

• infer-subhogs silently drops proteins (3% of all proteins on fungi-30)

  bug
  DessimozLab/FastOMA#113 · Filter by author alpae opened on Nov 4, 2026

• Multiple HOGs refer to the same OMAmer Root Hog

  DessimozLab/FastOMA#91 · Filter by author iantsang-ebi opened on Jul 15, 2026
  1

• Run stops after successful check_input

  DessimozLab/FastOMA#83 · Filter by author SamLlm opened on Jan 16, 2026
  2

• Can FastOMA infer orthologs between distantly related species?

  question
  DessimozLab/FastOMA#65 · Filter by author Yolanda1201 opened on Jun 6, 2025
  1

• HOG Gene content

  DessimozLab/FastOMA#63 · Filter by author esud1 opened on Mar 11, 2025
  1

• Process hog_big (127) terminated with an error exit status (130)

  DessimozLab/FastOMA#61 · Filter by author diekei opened on Feb 16, 2025
  10

• omamer_run terminated with an error exit status (254)

  DessimozLab/FastOMA#51 · Filter by author vincentkaiheng opened on Jan 13, 2025
  6

• gene with Expansion & Contraction

  question
  DessimozLab/FastOMA#50 · Filter by author Johnsonzcode opened on Jan 11, 2025
  6

• nextflow error

  DessimozLab/FastOMA#46 · Filter by author Song-10-YF opened on Jan 6, 2025
  7

• Avoid length limit for input fasta ids

  enhancement
  DessimozLab/FastOMA#30 · Filter by author alpae opened on Jul 24, 2024
  1