Ancestral Sequence Reconstruction

30-60 minutesPaperCodeProduction Ready

Reconstruct ancestral sequences from modern sequences

Readiness

Readiness: Production Ready
Smoke: passed
Artifacts: passed
Production: production_pass
Storage: <5
Strategy: shared python312_slim.sif + ancseq py312 target layer + staged IQ-TREE 3.1.3 binary
Next: Production Ready. Optional hardening: expose FASTA alignment upload, mode selector, outgroup, bootstrap, and fast/full IQ-TREE controls in the UI.

SOP main-thread triage cloned upstream YuSugihara/ancseq revision 2a62934edd2317f9d61738c88f710a90ef1efa49 at /media/nik/seagate_nik/bio_server/tools/ancestral-sequence-reconstruction/source; source about 16M. README requires IQ-TREE on PATH and Biopython. Slurm job 389 attempted bundled test/test_aa.fasta, but system Python blocked pip --user due PEP 668 externally-managed environment and the job produced no output; wrapper also depends on iqtree/iqtree2 being available. No production runner adapter/artifacts validated. 2026-07-08T23:33:30+08:00 SOP production validation: promoted from Production Blocked to Production Ready. Fixed backend IQ-TREE wrapper path to /media/nik/seagate_nik/bio_server, staged ancseq 1.3.0 + Biopython 1.85 + NumPy into /media/nik/seagate_nik/bio_server/tools/ancestral-sequence-reconstruction/py312_site, and reused shared python312_slim.sif plus IQ-TREE 3.1.3. Validated upstream YuSugihara/ancseq on bundled test/test_aa.fasta in AA mode with --fast through Ubuntu runner API job 17cf4ee92d27 / Slurm job 574. Run completed in 5.376 s and produced 13 ancestral sequence records, 1,101 ungapped sequence characters, 108 gap characters in the gap-aware FASTA, a 723-byte treefile, and 37,341-byte sorted probability TSV. Artifacts verified: summary.json, results.csv, input_alignment.fasta, ancestral_state_result.fasta, ancestral_state_result_with_gap.fasta, ancestral_state_result.treefile, ancestral_state_result.sort.tsv, ancestral_state_result.tsv, ancseq_stdout.txt, ancseq_stderr.txt, slurm.out, slurm.err.