bio-ecological-genomics-conservation-genetics
Assesses genetic health of populations for conservation using effective population size estimation (GONE2 for recent Ne trajectory, NeEstimator for contemporary Ne, Stairway Plot 2 and PSMC for historical Ne), F-statistics (hierfstat), runs of homozygosity (detectRUNS), and genetic diversity metrics. Use when estimating effective population size, detecting inbreeding or bottlenecks, or assessing genetic diversity in threatened species from microsatellite or SNP data.
npx skills add BioTender-max/awesome-bio-agent-skills --skill conservation-genetics --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: bcftools 1.19+ Before using code patterns, verify installed versions match. If versions differ: - 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. # Conservation Genetics **"Assess the genetic health of my endangered population"** → Estimate effective population size (Ne) trajectories, measure F-statistics and heterozygosity, detect inbreeding through runs of homozygosity, and reconstruct demographic history from SNP or microsatellite data. - R: `hierfstat::basic.stats()` for F-statistics and diversity - R: `detectRUNS::consecutiveRUNS.run()` for ROH detection - CLI: `gone2` for recent Ne trajectory from phased genotypes Assesses genetic health of populations through diversity metrics, effective population size estimation, inbreeding detection, and demographic history reconstruction. ## Genetic Diversity with hierfstat Basic population genetics statistics using Weir & Cockerham estima
- Version Compatibility
- Genetic Diversity with hierfstat
- Pairwise Fst
- Allelic Richness
- Private Alleles
- Runs of Homozygosity (ROH)
- ROH Length Classes
- Effective Population Size (Ne)
- GONE2: Recent Ne Trajectory (Linkage Disequilibrium)
- NeEstimator: Contemporary Ne (LD Method)
- Stairway Plot 2: Demographic History from SFS
- PSMC: Whole-Genome Pairwise Coalescent
- Ne Interpretation Thresholds
- Bottleneck Detection
GONE2 is a standalone CLI tool (esrud/GONE2), not an R package Requires at least 10,000 SNPs and 50 individuals for reliable estimates Smaller -u focuses on more recent generations Step 1: Generate folded SFS from VCF Blueprint file specifies SFS, mutation rate, generation time Step 2: Run Stairway Plot 2 java -cp stairway_plot_v2.jar Stairbuilder blueprint.txt Step 3: Execute the generated bash script bash blueprint.sh Consensus FASTQ from BAM
What does the bio-ecological-genomics-conservation-genetics skill do?
Assesses genetic health of populations for conservation using effective population size estimation (GONE2 for recent Ne trajectory, NeEstimator for contemporary Ne, Stairway Plot 2 and PSMC for historical Ne), F-statistics (hierfstat), runs of homozygosity (detectRUNS), and genetic diversity metrics. Use when estimating effective population size, detecting inbreeding or bottlenecks, or assessing genetic diversity in threatened species from microsatellite or SNP data.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill conservation-genetics --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.