bio-comparative-genomics-introgression-detection
Detect introgression and admixture between species or populations using Dsuite (Malinsky 2021 fast D-statistics), Patterson's D / ABBA-BABA test (Green 2010; Durand 2011), f4-ratio and f-branch statistic (Malinsky 2018), TreeMix (Pickrell & Pritchard 2012), HyDe (Blischak 2018), QuIBL (Edelman 2019), sprime (Browning 2018), Twisst (Martin 2017), PhyloNet (Solis-Lemus 2017) for explicit phylogenetic networks, and qpAdm / qpGraph (Patterson 2012; Lipson 2013). Distinguish introgression from incomplete lineage sorting (ILS), ancestral structure, ghost-lineage admixture, and rate variation. Use wh
npx skills add BioTender-max/awesome-bio-agent-skills --skill introgression-detection --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: Dsuite 0.5+ (millanek/Dsuite; Malinsky 2021 Mol Ecol Res 21:584; ABBAclustering option from Koppetsch-Malinsky-Matschiner 2024 Syst Biol), HyDe 0.4.3+ (Blischak 2018 Syst Biol 67:821), QuIBL (Edelman 2019 Science 366:594), TreeMix 1.13+ (Pickrell & Pritchard 2012 PLoS Genet 8:e1002967), sprime (Browning 2018 Cell 173:53), Twisst (Martin & Van Belleghem 2017 Genetics 206:429), PhyloNet 3.8.2+ (NakhlehLab/PhyloNet; Than-Ruths-Nakhleh 2008 BMC Bioinf 9:322) and PhyloNetworks 0.16+ (JuliaPhylo/PhyloNetworks; Solis-Lemus & Ane 2017 PLoS Comp Biol 13:e1005485), qpAdm / qpGraph (AdmixTools v2.0+; Maier 2023), ADMIXTOOLS2 R wrapper (Maier 2023 eLife 12:e85492), MaCS-like simulators (msprime 1.3+ for testing), bcftools 1.21+, samtools 1.21+, vcftools 0.1.16+, R 4.4+. See upstream Dsuite docs for visualization helpers. Before using code patterns, verify installed versions match. If versions differ: - CLI: `Dsuite --version`; `treemix --help`; `qpDstat --help` (AdmixTools) - Python: `pip show msprime hyde` - R: `packageVersion('admixtools')` If code throws `Dsuite SETS file format error`, `TreeMix matrix singular`, `qpAdm rotation faile
- Version Compatibility
- Algorithmic Taxonomy
- Decision Tree by Experimental Scenario
- Per-Method Failure Modes
- ILS confounded with introgression in D-statistic
- Ghost lineage admixture mimicking signal
- Ancestral structure (population subdivision before admixture)
- Outgroup-distance effect on D-statistic
- Sample-size bias in D-statistic
- TreeMix migration-edge selection
- qpAdm rotation failures
- Multiple-testing correction across population trios
- Genomic-window choice in Twisst / QuIBL
- Phylogenetic network not unique
cat > SETS.tsv << 'EOF' Real CLI flags (verify with `Dsuite Dtrios --help` against installed version): Fbranch is its own subcommand (`Dsuite Fbranch`); no Dtrios flag toggles it. Dsuite Dtrios \ population_genotypes.vcf.gz \ SETS.tsv Dsuite Fbranch species_tree.nwk trios_run_tree.txt > trios_run_fbranch.txt Implementation specifics depend on the Dsuite branch / fork distributing the ABBAclustering option; consult the Koppetsch 2024 supplement and `Dsuite --help` for current invocation. The option may be exposed as a subcommand or per-trio flag rather than a global Dtrios switch.
What does the bio-comparative-genomics-introgression-detection skill do?
Detect introgression and admixture between species or populations using Dsuite (Malinsky 2021 fast D-statistics), Patterson's D / ABBA-BABA test (Green 2010; Durand 2011), f4-ratio and f-branch statistic (Malinsky 2018), TreeMix (Pickrell & Pritchard 2012), HyDe (Blischak 2018), QuIBL (Edelman 2019), sprime (Browning 2018), Twisst (Martin 2017), PhyloNet (Solis-Lemus 2017) for explicit phylogenetic networks, and qpAdm / qpGraph (Patterson 2012; Lipson 2013). Distinguish introgression from incomplete lineage sorting (ILS), ancestral structure, ghost-lineage admixture, and rate variation. Use wh
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill introgression-detection --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.