Positive Selection

What the source does

• FilesystemNone observedNo reads or writes in the source
• NetworkNone observedNo outbound calls in the source
• ShellNone observedNo commands run in the source
• DependenciesPinnedNothing floats
• SecretsNone foundNo keys in source

Five audit layers

Gates applied: no behavioural pass.

Audit 0.4.1 · source sha c8c1fc3a2b13 · 19 Oct 2026Report an issue or request a re-scan

• PublisherGPTomics GitHub organizationOwner of the repository this skill is read from
• Source folderGPTomics/bioSkills/comparative-genomics/positive-selectionThe exact folder we audited
• LicenceMITAs the repository states it
• Commit pinned for this verdictc8c1fc3a2b13A new audit runs when the source changes
• Repository statusArchivedLast push 65 days ago
• Sandboxed runNot runSkills are read, not executed; layer L4 is skipped

Its description: Detect positive (diversifying / episodic / pervasive) selection using codon dN/dS frameworks. Implements PAML codeml site models (M0/M1a/M2a/M7/M8/M8a), branch models, branch-site model A (Zhang 2005), and HyPhy methods…

---
name: bio-comparative-genomics-positive-selection
description: Detect positive (diversifying / episodic / pervasive) selection using codon dN/dS frameworks. Implements PAML codeml site models (M0/M1a/M2a/M7/M8/M8a), branch models, branch-site model A (Zhang 2005), and HyPhy methods (BUSTED, BUSTED-S, BUSTED-MH, BUSTED-PH, MEME, FEL, FUBAR, aBSREL, SLAC, RELAX, GARD, FUBAR-MH). Includes McDonald-Kreitman framework (asymptotic alpha, impMKT, polyDFE, DFE-alpha, GRAPES) for within-species + divergence inference, RERconverge for trait-correlated rate shifts, CSUBST for convergent substitution, and PhyloAcc for accelerated noncoding evolution. Use when testing adaptive evolution at codons, branches, or full gene; running GARD recombination pre-screen; controlling alignment-error and gBGC false positives; reconciling PAML vs HyPhy results; or performing genome-scale selection scans.
tool_type: mixed
primary_tool: PAML
---

## Version Compatibility

Reference examples tested with: PAML 4.10.7+, HyPhy 2.5.62+ (BUSTED-MH from Lucaci 2023 MBE 40:msad150; FUBAR-MH from same), datamonkey.org 2024+ for web jobs, IQ-TREE 2.3.6+, MACSE V2.07+, PRANK 170427+, MAFFT 7.526+, PREQUAL 1.02+, HmmCleaner 0.243+, GARD (HyPhy bundled), RDP5 5.59+, ete4 4.1.0+, BioPython 1.84+, scipy 1.13+, polyDFE 2.0+, DFE-alpha 2.16+, GRAPES 1.1.1+, RERconverge 0.3.0+, CSUBST 1.6.0+, PhyloAcc 2.4.0+. Quest-for-Selection benchmark refreshed annually.

Before using code patterns, verify installed versions match. If versions differ:
- CLI: `codeml` (PAML; check by `codeml /dev/null` -- prints version banner), `hyphy --version`, `gard --help`
- Python: `pip show pyhyphy`; introspect ete4 API for tree-labeling
- R: `packageVersion('RERconverge')`; `?correlateWithBinaryPhenotype`

If code throws `branch-site test LRT non-positive`, `omega2 hit upper bound 999`, `MEME ML mixed gradient`, the most common cause is alignment error or saturated dS -- inspect alignment with TCS / Guidance2 and dS-vs-divergence-time. PAML 4.10 changed several control-file keywords from 4.9 (`getSE = 1` syntax tightened).

# Positive Selection Analysis

**"Is this gene / branch / site under positive selection?"** -> dN/dS (omega = nonsynonymous-to-synonymous substitution rate ratio) framework with explicit choice of WHICH question is being asked (gene-wide / branch-specific / site-specific / episodic) and WHICH null is being rejected. The "test failed because of selection" claim has more known confounders than any other comparative-genomics inference; **mandatory pre-screens are: recombination (GARD), alignment errors (PREQUAL or HmmCleaner), saturation (dS distribution), and gBGC (W->S substitution bias)**. Skipping any one inflates Type-I error to ~20-50% (Anisimova & Yang 2007 MBE 24:1219; Pond 2006 Mol Biol Evol 23:1891).

- CLI: `codeml` PAML site, branch, branch-site models
- CLI: `hyphy busted` `hyphy meme` `hyphy fel` `hyphy fubar` `hyphy absrel` `hyphy relax` `hyphy gard`
- Web: datamonkey.org for HyPhy jobs without local install
- R: `RERconverge::correlateWithBinaryPhenotype()` for trait-rate associations
- CLI: `csubst analyze` for convergent substitution
- R/CLI: `phyloacc` for noncoding accelerated evolution

## Algorithmic Taxonomy

| Method | Question | Null model | Strength | Fails when |
|--------|----------|------------|----------|------------|
| PAML codeml M0 (Yang 1997 CABIOS 13:555) | Gene-wide single-omega estimate | -- (point estimate) | Standard reference omega; baseline test | Site heterogeneity (use M3+) |
| codeml M1a vs M2a (Yang 2000 Genetics 155:431) | Any site under selection? | Nearly neutral, 2-category | Conservative; LRT df=2 | Low power for episodic selection |
| codeml M7 vs M8 | More-sensitive site test | Beta(0,1) | Higher power than M1a/M2a | Higher false-positive rate; relaxed-constraint mimics selection |
| codeml M8 vs M8a (Swanson 2003 MBE 20:18) | Conservative site test (omega2 = 1 null) | Beta + omega2=1 | Cleanest LRT df=1; preferred site test | Lower power than M7 vs M8 |
| codeml branch-site mod A (Zhang 2005 MBE 22:2472) | Selection on pre-specified foreground branch | A1 (omega2=1 fixed) | Most powerful for episodic per-branch selection | Foreground specified post hoc -> Type-I inflation |
| codeml clade model (Bielawski & Yang 2004 J Mol Evol 59:121) | Different omega between named clades | M3 with shared categories | Tests for shifted selection regime | Requires clade pre-specification |
| codeml free-ratio | Per-branch omega estimates (exploratory) | M0 | Visualizes branch-wise variation | Unidentifiable for short branches; no formal LRT |
| HyPhy BUSTED (Murrell 2015 MBE 32:1365) | Any episodic selection on any branch site? | No omega+ class | Site + branch joint; foreground assignable | Sensitive to alignment errors |
| HyPhy BUSTED-S (Wisotsky 2020 MBE 37:2430) | BUSTED with synonymous-rate variation | -- | Corrects for SRV; reduces false positives | Slightly less power than BUSTED |
| HyPhy BUSTED-MH (Lucaci 2023 MBE 40:msad150) | BUSTED with multi-nucleotide substitutions | -- | Captures complex (multi-hit) substitutions; reduces false positives from MNMs | Newer; limited benchmarking |
| HyPhy BUSTED-PH | Two phenotypes; selection on one not other | -- | Tests phenotype-specific selection | Requires phenotype branch label |
| HyPhy MEME (Murrell 2012 PLoS Genet 8:e1002764) | Per-site episodic selection | FEL | Detects sites under episodic positive selection | Higher false-positive rate at p threshold |
| HyPhy FEL (Kosakovsky Pond 2005 MBE 22:1208) | Per-site pervasive selection | -- | Fast; counts substitutions per site | No episodic detection |
| HyPhy FUBAR (Murrell 2013 MBE 30:1196) | Bayesian per-site pervasive selection | -- | Scales to 1000s of sequences; posterior probability | No episodic detection |
| HyPhy SLAC | Counting-based fast estimator | -- | Very fast; rough estimate | Lower power; no statistical model |
| HyPhy aBSREL (Smith 2015 MBE 32:1342) | Branch-specific selection w

Excerpt, first 6,000 characters of SKILL.md, verbatim from the audited commit. It is text from someone else’s repository, quoted so you can judge it before your agent reads it.

pip install ete4 pyhyphy csubst
pip install csubst
pip install ete4 pyhyphy

git clone https://github.com/GPTomics/bioSkills
git -C bioSkills checkout c8c1fc3a2b13

Works in

1. 2026-10-19
   ✓SAFE B 89 / 100

   first audit · source c8c1fc3a2b13

Questions about Positive Selection

• github.com/GPTomics/bioSkills/tree/main/comparative-genomics/pos — the audited source at commit c8c1fc3a2b13 and every finding aboveObserved · 19 Oct 2026

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