Attribution

Generated 2026-09-29 by scripts/attribution_doc.py. OpenBiota redistributes none of the software or data below: each is fetched from its publisher at install time and pinned by version and checksum under refs/expanded/. Every run records the exact versions and release identifiers it used in results.json (detection.reference_releases, run) and in run.log. Licences are as each project publishes them at the time of writing; check the source before any commercial use, and note that the MetaPhlAn databases and BacDive carry noncommercial or contact-first terms of their own.

Software

tool	used for	licence	home
DIAMOND	translated search of every read against the metabolite gene panels	GPL-3.0	https://github.com/bbuchfink/diamond
Bowtie2	host-read removal; competitive confirmation alignments	GPL-3.0	https://github.com/BenLangmead/bowtie2
samtools	alignment sorting, indexing and depth	MIT/Expat	https://github.com/samtools/samtools
MetaPhlAn 3.1	the scoring lane the reference cohort and GMWI2 were built with	MIT	https://github.com/biobakery/MetaPhlAn
MetaPhlAn 4 (Jun23, Jan26), StrainPhlAn 4, sample2markers	species-level genome bins; comparative strain placement	MIT (software); CHOCOPhlAn databases CC BY-NC-SA	https://github.com/biobakery/MetaPhlAn
PhyloPhlAn, RAxML	marker alignment and tree inference inside StrainPhlAn	MIT; GPL-3.0	https://github.com/biobakery/phylophlan
sylph	whole-genome containment against GTDB R232 and GlobDB r232	MIT	https://github.com/bluenote-1577/sylph
mOTUs 4.1	universal single-copy marker profiling	GPL-3.0	https://github.com/motu-tool/mOTUs
Kraken 2, Bracken	read classification against UHGG v2.0.2 and the gut rescue panel	MIT; GPL-3.0	https://github.com/DerrickWood/kraken2
SingleM (with OrfM, smafa, mfqe, HMMER)	marker-window profiling of lineages no catalogue names	GPL-3.0 (SingleM, HMMER); MIT (OrfM, smafa, mfqe)	https://github.com/wwood/singlem
metaSPAdes	targeted assembly of reads no method could place	GPL-2.0	https://github.com/ablab/spades
skani, FastANI	genome-wide ANI for supplement reconciliation	MIT; Apache-2.0	https://github.com/bluenote-1577/skani
seqkit	read selection for targeted assembly; marker extraction	MIT	https://github.com/shenwei356/seqkit
aria2	parallel, resumable reference downloads	GPL-2.0-or-later	https://aria2.github.io
fastp	read QC and trimming	MIT	https://github.com/OpenGene/fastp
GMWI2	the published gut-health index	MIT	https://github.com/danielchang2002/GMWI2
MICOM (with HiGHS, OSQP)	model-assisted metabolic scenarios	Apache-2.0; MIT; Apache-2.0	https://github.com/micom-dev/micom
ReportLab	the PDF	BSD-3-Clause	https://www.reportlab.com/opensource/
NumPy, PyYAML, scikit-learn	arithmetic, configuration, the age model	BSD-3-Clause; MIT; BSD-3-Clause	https://numpy.org
curatedMetagenomicData	the 3,027-adult reference cohort's profiles and metadata	Artistic-2.0	https://waldronlab.io/curatedMetagenomicData/
AGORA2 / VMH	genome-scale metabolic models behind the scenarios	CC BY 4.0	https://www.vmh.life
BacDive (DSMZ)	culture-collection identities and reference-strain traits, via API v2	CC BY 4.0; DSMZ asks to be contacted for commercial use	https://bacdive.dsmz.de
UniProt	reference proteins for the metabolite gene panels	CC BY 4.0	https://www.uniprot.org

Reference releases

Each lock file under refs/expanded/locks/ carries the URLs, sizes, SHA-256 digests and retrieval date.

source	release	licence	home
elgg	ELGG (Zenodo 6969520) (2,172 species representative)	CC BY 4.0 (Zenodo record 6969520)	https://zenodo.org/records/6969520/files
globdb_genomes	globdb_r232 (346,233 representative genome)	CC BY-SA 4.0	https://fileshare.lisc.univie.ac.at/globdb/globdb_r232
globdb_r232	globdb_r232 (346,233 species representative)	CC BY-SA 4.0 (GlobDB); index by sylph authors	https://fileshare.lisc.univie.ac.at/globdb/globdb_r232/taxonomic_profiling
gtdb_r207	R207	CC BY-SA 4.0	https://data.gtdb.ecogenomic.org/releases/release207/207.0/auxillary_files
gtdb_r220	R220	CC BY-SA 4.0	https://data.gtdb.ecogenomic.org/releases/release220/220.0/auxillary_files
gtdb_r226	R226	CC BY-SA 4.0	https://data.gtdb.ecogenomic.org/releases/release226/226.0/auxillary_files
gtdb_r232	R232 (901,341 genome)	CC BY-SA 4.0	https://data.gtdb.ecogenomic.org/releases/release232/232.0
hrgm2	HRGMv2 (4,824 species representative)	CC BY 4.0 (Zenodo record 19482781)	https://zenodo.org/records/19480672/files
hrom	HROM	see file	https://www.decodebiome.org/HROM/data/genome_catalog
humgut2	HumGut2 (31,225 genome (97.5% ANI dereplicated))	CC BY 4.0 (authors)	https://arken.nmbu.no/~larssn/humgut
motus_db	mOTUs DB 4.1 (Zenodo 20322482)	CC BY 4.0 (mOTUs data)	https://zenodo.org/records/20322482/files
mpa_jan26	mpa_vJan26_CHOCOPhlAnSGB_202605 (72,000 SGB)	MIT (MetaPhlAn); database CC BY-NC-SA per bioBakery	https://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases
sgb_bridges	MetaPhlAn utils @ master 2026-09	MIT (MetaPhlAn)	https://raw.githubusercontent.com/biobakery/MetaPhlAn/master/metaphlan/utils
singlem_globdb	GlobDB_r232.metapackage_v4	CC BY-SA 4.0	https://fileshare.lisc.univie.ac.at/globdb/globdb_r232/taxonomic_profiling
uhgg_kraken2	v2.0.2 (4,744 species)	EMBL-EBI terms of use	https://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0.2/kraken2_db_uhgg_v2.0.2
uhgg_v2.0.2	v2.0.2 (289,232 genome)	EMBL-EBI terms of use (open)	https://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0.2

Published research

Every metabolite pathway, disease-pattern profile, microbial group, organism description and intervention assertion names the study it rests on (DOI or PubMed identifier) in its definition file and on the page of the report where it is used. The complete catalogue of sources is on the website's research page and in specs/research/.