bio-phylo-divergence-dating
Estimate divergence times using molecular clock models with BEAST2, MCMCTree, and TreePL. Use when dating speciation events, calibrating phylogenies with fossils, choosing between strict and relaxed clock models, or estimating evolutionary rates across lineages.
npx skills add BioTender-max/awesome-bio-agent-skills --skill divergence-dating --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: BEAST2 2.7+, MCMCTree (PAML 4.10+), TreePL 1.0+, Python 3.9+ Before using code patterns, verify installed versions match. If versions differ: - CLI: `beast -version` then `beast -help` to confirm flags - CLI: `mcmctree --help` or check PAML documentation for parameter names - CLI: `treePL` to confirm installation - Python: `pip show biopython` then `help(module.function)` to check signatures If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Divergence Time Estimation **"Estimate when lineages diverged"** -> Combine phylogenetic trees with fossil calibrations and molecular clock models to infer absolute divergence times. - CLI: BEAUti + BEAST2 for moderate data with complex models - CLI: MCMCTree (PAML) for genome-scale data with approximate likelihood - CLI: TreePL for very large trees with penalized likelihood ## Clock Model Selection | Model | Assumption | When to Use | |-------|------------|-------------| | Strict clock | Constant rate across all lineages | Only when a molecular clock test does not reject clocklik
- Version Compatibility
- Clock Model Selection
- Clock Model Diagnostics
- Fossil Calibration Strategies
- Node Calibration (Traditional)
- Critical Calibration Pitfalls
- Tip-Dating and Fossilized Birth-Death (FBD)
- FBD vs Node Calibration
- Software Decision Framework
- BEAST2 Dating Workflow
- Step-by-Step Workflow
- BEAST2 Clock Rate Prior
- Key BEAST2 Packages
- MCMCTree Workflow
Rough clock rate estimation: rate = divergence / (2 * time) For mammals: ~0.01 substitutions/site/Myr for nuclear genes For mitochondrial: ~0.02 substitutions/site/Myr Set lognormal prior with M = ln(expected_rate), S = 0.5-1.0 Step 1: Generate gradient and Hessian (in.BV file) Set usedata = 3 in control file, then run: mcmctree mcmctree_step1.ctl Step 2: Run MCMC with approximate likelihood Set usedata = 2 in control file, then run:
What does the bio-phylo-divergence-dating skill do?
Estimate divergence times using molecular clock models with BEAST2, MCMCTree, and TreePL. Use when dating speciation events, calibrating phylogenies with fossils, choosing between strict and relaxed clock models, or estimating evolutionary rates across lineages.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill divergence-dating --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.