bio-ecological-genomics-species-delimitation
Delimits species boundaries from molecular data using distance-based (ASAP), tree-based (bPTP, GMYC), and coalescent (BPP) methods. Compares multiple delimitation results with delimtools. Use when delineating putative species from DNA barcoding data, resolving cryptic species complexes, or validating taxonomic assignments. Emphasizes multi-method consensus following integrative taxonomy best practice.
npx skills add BioTender-max/awesome-bio-agent-skills --skill species-delimitation --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: BioPython 1.83+, numpy 1.26+, scipy 1.12+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Species Delimitation **"Delineate species boundaries from my DNA barcoding data"** → Apply multiple delimitation methods (distance-based ASAP, tree-based bPTP/GMYC, coalescent BPP) to molecular data and compare results for multi-method consensus following integrative taxonomy best practice. - CLI: ASAP web tool or standalone for distance-based partitioning - Python: bPTP via `PTP-pyqt5` for Bayesian branching-rate analysis - R: `splits::gmyc()` for coalescent/speciation transition model Delimits putative species from molecular data using complementary distance-based, tree-based, and coalescent methods. ## Overview of Methods | Method
- Version Compatibility
- Overview of Methods
- ASAP (Assemble Species by Automatic Partitioning)
- Interpreting ASAP Results
- Python ASAP-Style Analysis
- bPTP (Bayesian Poisson Tree Processes)
- Interpreting bPTP Output
- GMYC (Generalized Mixed Yule Coalescent)
- Multiple-Threshold GMYC
- GMYC Visualization
- BPP (Bayesian Phylogenetics and Phylogeography)
- Interpreting BPP Results
- Multi-Method Comparison
- Ultrametric Tree Preparation
ASAP web interface: https://bioinfo.mnhn.fr/abi/public/asap/asapweb.html Upload aligned FASTA, select distance model Command-line ASAP (if available) ASAP -i aligned_sequences.fasta -d K2P -o asap_results/ iTaxoTools PTP (Python 3 compatible) pip install PTP-pyqt5 Run bPTP from command line python -m PTP.PTP -t rooted_tree.nwk -o bptp_results \
What does the bio-ecological-genomics-species-delimitation skill do?
Delimits species boundaries from molecular data using distance-based (ASAP), tree-based (bPTP, GMYC), and coalescent (BPP) methods. Compares multiple delimitation results with delimtools. Use when delineating putative species from DNA barcoding data, resolving cryptic species complexes, or validating taxonomic assignments. Emphasizes multi-method consensus following integrative taxonomy best practice.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill species-delimitation --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.