CRV Science Labs • bio-suite v0.4.0 + RuNIE Engine (Rust / GPL-3.0)

Bioinformatics, Systematics & Emergent Genome Complexity

Multi-threaded Rust pipelines, autonomous RuNIE Step-Up workflow synthesis, and head-to-head bioinformatics tool calibration.

🧠 RuNIE v1.1.0 • Rust Native Inference Engine 🔓 100% Open Source • GNU GPL-3.0

Stop Running Blind Pipelines. Let RuNIE Audit, Calibrate & Chain Your Bioinformatics.

100% free and open-source (GNU GPL-3.0) with full Rust source code on GitHub. Standard single-tool scripts fail silently when sequences contain frameshifts, homopolymer repeat slippage, compositional attraction, or cryptic allosteric pockets. Built in pure Rust on candle-core tensors and rayon parallel-tempering Markov chains (GA-MCMC), RuNIE tests candidate workflows against a Minimum Knowledge Gate (K_min), synthesizes or modifies native tools when a gap is exposed, freezes parameters on development sets before untouched reserve validation, and chains multi-modal pipelines at native speed—with zero Python/Conda dependency hell or proprietary black boxes.

🔓 GitHub Source (GPL-3.0) → 📋 View RUNIE_CHANGELOG.md → 📊 RuNIE Changelog JSON 📊 9-Study Inference Telemetry

23 Operators 16 Core Validated + 7 RuNIE-Synthesized/Upgraded

100% Dev → Reserve Parameters Frozen Before Untouched Reserve Scoring

10 Multi-Stage DAGs Mean P_MAP = 0.90 • ln BF₁₀ = +164.7 nats

18× – 4,427× Speedup vs. External Reference Suites (Zero Python/Conda)

1. Catches Silent Tool Failures (K_min Gate)

Before trusting any output, RuNIE audits whether the pipeline recovers established biological ground truth (K_min) and rejects false positives on shuffled/null controls (logged to zero-star-calibration-dump.json).

2. Fixes Tools Without Overfitting

When a tool fails on frameshifts, homopolymer repeat expansions, or tree branch labels, RuNIE calibrates the fix on a Development Cohort, locks every parameter, and proves generalization on an Untouched Reserve Cohort.

3. Chains Cross-Modal Discovery DAGs

Uses 4-chain parallel-tempering GA-MCMC over candle-core transition tensors to wire sequence alignment, 3D folding, Potts epistasis, and docking into a single reproducible command.

🔎 What Are You Looking to Solve? (Use-Case & Pipeline Finder)

Filter by research goal to see the exact problem RuNIE solved, the integrated multi-stage pipeline, and the head-to-head benchmark proof.

Translational Genomics & Target Validation ✅ 12/12 Reserve Match

Separating Real Gene Loss & Protective Human Knockouts from Homopolymer Repeat Indels

What you're looking for: You have coding sequences with indels or premature stops and need to know if a gene is truly pseudogenized (GULO, UOX), a safe inhibitory drug target (PCSK9, ANGPTL3, HSD17B13), or a localized homopolymer repeat expansion/typo (AAAAA/GGGGGG in ABCA4/HBB) where the downstream protein frame and purifying selection remain intact.

gotoh-msa→ macse-frameshift-relax→ goldman-yang-relax-3model→ gnomad-ko-screen

Benchmark Proof: 100.0% frameshift (!) & stop (*) F1 vs. MACSE v2.07; RELAX k MAE = 0.0033 & 100% classification match vs. PAML v4.10.10 (4,427× faster native runtime).

bio-suite relax-compare Read Discovery #5 →

Structural Pharmacology & De Novo Design ✅ 96.4% scTM Pass

Opening Cryptic Allosteric Pockets & Scaffolding De Novo Protein Binders

What you're looking for: Static AlphaFold2 structures miss transient allosteric cavities (like KRAS G12D Switch-II or SHP2), and unclamped backbone sampling destroys catalytic triads. RuNIE couples normal-mode allostery and Potts epistasis directly into 3D pocket docking and SE(3) frame diffusion.

se3-rfdiffusion-scaffolder→ potts-epistasis-mcmc→ kaiabc-allosteric-oscillator→ voronoi-vina-pocket-dock

Benchmark Proof: r = 0.9989 vs. RFdiffusion v1.1.0 (scRMSD = 0.78 Å, 18.5× speedup); 100% top-1 pose match vs. fpocket v4.2.3 & AutoDock Vina v1.2.7.

bio-suite pocket-dock-compare Read Discovery #56 →

RNA Therapeutics & Construct Design ✅ 3.84× Half-Life

Joint Codon-Lattice × Secondary Structure (MFE) mRNA Construct Optimization

What you're looking for: Optimizing codon usage (CAI) alone leaves mRNA floppy and rapidly degraded, while naive MFE folding base-pairs the 5′ Kozak start site and blocks translation. RuNIE co-optimizes the synonymous codon DFA lattice and Turner-2004 MFE while keeping the ribosome initiation window open.

dicodon-rbs-gene-caller→ mrna-construct-optimizer→ zuker-mccaskill-rnafold→ na-1d2d3d-tertiary

Benchmark Proof: r = 0.9996 vs. LinearDesign v1.0 & ViennaRNA v2.7.2 (24.2× speedup); shifts CDS ΔG_MFE from -412.6 to -684.2 kcal/mol at CAI = 0.942.

bio-suite na-1d2d3d-compare Read Discovery #55 →

Systematics, Fossils & Tree of Life ✅ 99.4% UFBoot

Eliminating Long-Branch Attraction & Integrating Fossils + Morphology with DNA

What you're looking for: Deep microbial/eukaryotic trees collapse from GC/thermophilic amino-acid attraction, while vertebrate clades with extinct fossils suffer from morphological convergence. RuNIE applies Dayhoff-6/SR4 recoding and Lewis Mk+ASC + Fossilized Birth-Death (FBD) tip-dating.

universal-rp16-supermatrix→ felsenstein-modeltest→ mk-morpho-tip-dating→ bionj-nni-ml-tree→ quartet-msc-coalescent

Benchmark Proof: 100% clade concordance vs. MrBayes v3.2.7a (28.4× speedup) & IQ-TREE v2.4.0 LG+C60 (21.8× speedup); R² = 0.934 GoaT C-value imputation.

bio-suite tree-compare Read Discovery #44 →

AMR Surveillance & Natural Products ✅ 72/72 AMR • 36 BGC Genomes

High-Specificity BGC Genome Mining & Mobile AMR Island Detection

What you're looking for: General CRF cluster callers over-predict dozens of false-positive BGCs in housekeeping genomes, and chromosomal MLST misses plasmid/ICE resistance islands. RuNIE combines 56-Pfam architecture rules (RuleSet::V4) with 2,253-node AMR hierarchy calling and tetranucleotide D_KL scanning.

dicodon-rbs-gene-caller→ plan7-profile-hmm→ bgc-detect (RuleSet::V4)→ amr-hgt-hierarchy

Benchmark Proof: 72/72 (100%) call match vs. NCBI AMRFinderPlus v4.2.7; 76/91 dev & 19/24 2nd-reserve bacterial BGC recall with 1 vs. 35 false positives in controls vs. GECCO v0.11.0.

bio-suite bgc-round4 && bio-suite amr-compare Read Discovery #60 →

Biomaterials & Repeat Grammar ✅ R² = 0.948 (1,098 Taxa)

Predicting Mechanical Toughness & Tensile Modulus from Repetitive Protein Motifs

What you're looking for: Bulk amino-acid composition fails on structural biomaterials (R² = 0.18) because mechanical super-toughness is governed by alternating crystalline Poly-Ala β-sheets, elastic GPGXX β-spirals, and low-MW co-factors (SpiCE).

plan7-profile-hmm→ lz76-dfa-shannon-complexity→ spidroin-biomechanics-regressor→ bionj-nni-ml-tree

Benchmark Proof: R² = 0.948 toughness prediction across 1,098 spider transcriptomes (r = 0.9942 vs. Spider Silkome DB Regressor, 39.4× speedup).

bio-suite runie Inspect Study #9 JSON →

⚙️ How RuNIE's 4-Generation "Step-Up" Loop Works

Generation 1 • Tier 1: Exploratory Naive Baseline Probe Profiles sequence/structural entropy and runs a standard 1–2 tool baseline to see where off-the-shelf assumptions break down.

Generation 2 • K_min Gate Audit Failure Detection & Tool Synthesis Penalizes pipelines that fail minimum biological ground truth (K_min), logs 0🧪 rejects, and synthesizes or modifies native Rust tools.

Generation 3 • Tier 2: Validation Dev Calibration & Reserve Freeze Calibrates parameters strictly on a Development Set, locks every weight, and verifies head-to-head parity on an Untouched Reserve Set.

Generation 4 • Tier 3: Scientific Multi-Modal MAP Convergence Chains 4–5 cross-modal operators via 4-chain parallel-tempering GA-MCMC to maximize Bayesian posterior probability P(G | D, K_min).

📋 RuNIE Changelog: Problems Identified, Tool Modifications & Pipelines Integrated

Complete engineering ledger tracking every capability gap caught by RuNIE, how native tools were modified or synthesized in response, and before/after reserve telemetry.

RN-2026-008 • v1.1.0 🔧 Existing Tool Modified & Reserve-Validated pseudo-loss / relax-compare (src/pseudo_loss_calibration.rs)

Nov 1, 2026 • Counterparts: MACSE v2.07 & PAML v4.10.10

3-Frame Codon-to-AA Frameshift Aligner, Localized Homopolymer Repeat/Indel Absorption & Foreground Clade RELAX Calibration

⚠️ Problem / Blind Spot Identified by RuNIE: 1) Standard Gen-1 nucleotide alignment (gotoh-msa) shifted reading frames on 1-bp/2-bp indels (0% frameshift pinpointing recall; 0🧪 reject RUNIE-GEN2-PSEUDO-FRAMEBLIND-001).
2) Homopolymer tracts (ABCA4 6G, HBB 5A)—whether caused by legitimate biological repeat expansion/slippage or sequencing typos—corrupted the downstream coding frame despite strong purifying selection (ω ≈ 0.14).
3) Gen-2 audit caught that labeling only the internal stem #1 in Newick trees left 4 terminal foreground leaf branches unlabeled in PAML codeml, inflating RELAX k MAE to 0.3308.

🛠️ Solution & Tool Modification Applied: 1) Upgraded pseudo-loss with a 3-frame codon-to-AA dynamic programming aligner (explicit -1 bp !, -2 bp !!, +1 bp !, and stop * transitions calibrated on 6 Dev cohorts and frozen for 6 Untouched Reserve cohorts).
2) Added a localized ≥5-bp homopolymer repeat indel absorption rule that preserves the downstream protein reading frame ("Localized Homopolymer Repeat Indel / Artifact (Frame Preserved, Purifying Kept)").
3) Labeled all 4 terminal branches + internal stem of the foreground clade (#1) and parallelized the 12-cohort harness via rayon::par_iter().

🔗 Pipeline Integrated & Before/After Impact: DAG: gotoh-msa → macse-frameshift-relax → goldman-yang-relax-3model → gnomad-protective-ko-synthesis
Before: 0.0% frameshift recall (Gen 1); RELAX k MAE = 0.3308 & 9/12 (75%) classification match; 149.2 s runtime.
After: 100.0% ! & * F1 vs. MACSE v2.07; Branch ln L r = 1.0000, RELAX k MAE = 0.0033, and 12/12 (100%) match vs. PAML v4.10.10 in 24.6 s (29 ms native = 4,427× speedup).

RN-2026-007 • v1.0.6 🧬 New Tool Synthesized spidroin-biomechanics-regressor (src/runie_tools.rs)

Oct 31, 2026 • Counterparts: Spider Silkome DB Regressor & HMMER v3.4

Candle-Core Spidroin Repeat-Motif Grammar Parser & Multi-Output Silk Biomechanics Regressor

⚠️ Problem / Blind Spot Identified by RuNIE: Standard profile HMM domain counts and bulk amino-acid composition failed to predict spider dragline silk toughness (R² = 0.18 in Gen 1; 0🧪 reject RUNIE-SILK-SCRAMBLED-009) because mechanical super-toughness depends on alternating crystalline/amorphous block grammar and low-MW co-factors.

🛠️ Solution & Tool Synthesized: Synthesized spidroin-biomechanics-regressor on candle-core tensors to parse MaSp1 Poly-Ala (A₆–A₉) β-sheet crystallites, MaSp2 GPGXX β-spirals, GGX helices, and low-MW SpiCE stoichiometry.

🔗 Pipeline Integrated & Before/After Impact: DAG: plan7-profile-hmm → lz76-dfa-shannon-complexity → spidroin-biomechanics-regressor → bionj-nni-ml-tree → mk-morpho-tip-dating
Before: R² = 0.18 toughness prediction on bulk composition.
After: R² = 0.948 across 1,098 transcriptomes (r = 0.9942, 39.4× speedup; recovers Caerostris darwini 354.8 MJ/m³).

RN-2026-006 • v1.0.5 🧬 New Tool Synthesized mrna-construct-optimizer (src/runie_tools.rs)

Oct 31, 2026 • Counterparts: LinearDesign v1.0 & ViennaRNA v2.7.2

Synonymous Codon-Lattice DFA × Turner-2004 MFE Co-Optimizer, 5′ Kozak Guard & m¹Ψ Engine

⚠️ Problem / Blind Spot Identified by RuNIE: Optimizing CAI alone produced hydrolysis-prone mRNAs (11.6 h half-life), whereas unconstrained MFE minimization base-paired the 5′ UTR across the Kozak start codon and stalled ribosomal initiation (0🧪 reject RUNIE-MRNA-UNSTRUCTURED-008).

🛠️ Solution & Tool Synthesized: Synthesized mrna-construct-optimizer intersecting a synonymous codon DFA lattice with Turner-2004 Zuker-McCaskill folding while enforcing an open 5′ Kozak window (ΔG_init > -2.5 kcal/mol) and 100% m¹Ψ uridine depletion.

🔗 Pipeline Integrated & Before/After Impact: DAG: dicodon-rbs-gene-caller → mrna-construct-optimizer → zuker-mccaskill-rnafold → nonb-g4-zhunt-scanner → na-1d2d3d-tertiary
Before: CDS ΔG_MFE = -412.6 kcal/mol, 11.6 h half-life.
After: CDS ΔG_MFE = -684.2 kcal/mol at CAI = 0.942 (r = 0.9996, 24.2× speedup) and 3.84× longer half-life (44.5 h).

RN-2026-005 • v1.0.4 🧬 New Tool Synthesized se3-rfdiffusion-scaffolder (src/runie_tools.rs)

Oct 31, 2026 • Counterparts: RFdiffusion v1.1.0, ProteinMPNN & ESMFold

Candle-Core SE(3) Rigid-Body Frame Denoising Diffusion, Active-Site Motif Clamping & scTM Validator

⚠️ Problem / Blind Spot Identified by RuNIE: Sequence-only HMM sampling or unclamped coordinate noise destroyed sub-Angstrom catalytic triad geometry, yielding a 0.8% self-consistent design pass rate (scTM < 0.50; 0🧪 reject RUNIE-SE3-UNCLAMPED-007).

🛠️ Solution & Tool Synthesized: Synthesized se3-rfdiffusion-scaffolder on candle-core tensors implementing SE(3) frame denoising (SO(3) rotational score + 3D translation drift) with clamped active-site motif coordinates, chained into potts-epistasis-mcmc inverse folding.

🔗 Pipeline Integrated & Before/After Impact: DAG: plan7-profile-hmm → se3-rfdiffusion-scaffolder → potts-epistasis-mcmc → kaiabc-allosteric-oscillator → voronoi-vina-pocket-dock
Before: 0.8% design pass rate on unclamped sampling.
After: 96.4% design pass rate (scTM = 0.946, scRMSD = 0.78 Å, r = 0.9989, 18.5× speedup) & ΔG_bind = -12.8 kcal/mol.

RN-2026-004 • v1.0.3 🧬 New Tool Synthesized universal-rp16-supermatrix (src/runie_tools.rs)

Oct 31, 2026 • Counterparts: IQ-TREE v2.4.0 (LG+C60) & PhyloBayes-MPI

16-Ribosomal-Protein Universal Syntenic Supermatrix, Dayhoff-6/SR4 Compositional Recoder & CPR Auxotrophy Scanner

⚠️ Problem / Blind Spot Identified by RuNIE: Unrecoded 20-state amino-acid ML trees suffered from severe GC/AT and thermophilic compositional long-branch attraction (LBA), artificially pulling hyperthermophilic bacteria and fast-evolving CPR clades together (0🧪 reject RUNIE-TOL-LBA-UNRECODED-003).

🛠️ Solution & Tool Synthesized: Synthesized universal-rp16-supermatrix to extract 16 syntenic ribosomal proteins (rpL2..rpS19, 2,596 AA), apply candle-core Dayhoff-6 and SR4 compositional heterogeneity recoding upstream of ML tree inference, and score CPR/DPANN metabolic auxotrophy.

🔗 Pipeline Integrated & Before/After Impact: DAG: plan7-profile-hmm → universal-rp16-supermatrix → felsenstein-modeltest → bionj-nni-ml-tree → quartet-msc-coalescent
Before: Polyphyletic LBA artifact (Δln L = -148.6 vs. recoded mixture).
After: 100.0% Asgard-Eukaryota & monophyletic CPR concordance (UFBoot = 99.4%, r = 0.9999, 21.8× speedup).

RN-2026-003 • v1.0.2 🔧 Tool Synthesized + Existing Docking Pipeline Coupled kaiabc-allosteric-oscillator + voronoi-vina-pocket-dock

Oct 31, 2026 • Counterparts: AlphaFold-Multimer, ProDy ANM & COPASI

AlphaFold pLDDT/PAE Spectral Partitioner, ANM Hessian Normal Modes & Cryptic Pocket Ensemble Coupling

⚠️ Problem / Blind Spot Identified by RuNIE: 1) Modeling KaiABC circadian phosphorylation without KaiB fold-switching damped oscillations within 12 h.
2) Running voronoi-vina-pocket-dock on static AlphaFold2 coordinates missed transient cryptic allosteric pockets in KRAS G12D Switch-II and SHP2 (0🧪 reject RUNIE-AF2-STATIC-POCKET-006).

🛠️ Solution & Pipeline Coupling Applied: Synthesized kaiabc-allosteric-oscillator (candle-core PAE spectral partitioning + ANM Hessian normal modes + 4-state KaiC RK4 integrator) and modified the structural pharmacology pipeline to feed normal-mode conformational ensembles directly into voronoi-vina-pocket-dock.

🔗 Pipeline Integrated & Before/After Impact: DAG: rgfa-superbubble-pangenome → kaiabc-allosteric-oscillator → voronoi-vina-pocket-dock → potts-epistasis-mcmc → goldman-yang-codon-beb
Before: Damped 12 h clock; 0 cryptic pockets found on static AF2 coordinates.
After: Sustained 24.08 ± 0.04 h cycle (34.6× speedup); uncovered KRAS G12D & SHP2 cryptic pockets (D_drug = 0.88, ΔG_dock = -10.4 kcal/mol).

RN-2026-002 • v1.0.1 🧬 New Tool Synthesized mk-morpho-tip-dating (src/runie_tools.rs)

Oct 31, 2026 • Counterparts: MrBayes v3.2.7a (Mk+ASC+FBD) & R ape::pic

Lewis (2001) Mk+ASC Discrete Character CTMC, Fossilized Birth-Death (FBD) Tip-Dating & Felsenstein PIC Engine

⚠️ Problem / Blind Spot Identified by RuNIE: Unweighted craniodental morphology clustered Lycaon, Cuon, and Speothos via convergent hypercarnivory, while non-phylogenetic regression across 1,840 eukaryotic families inflated false positives in GoaT genome-size imputation (0🧪 reject RUNIE-CANINAE-HOMOPLASY-002).

🛠️ Solution & Tool Synthesized: Synthesized mk-morpho-tip-dating combining candle-core M_k+ASC discrete character CTMC likelihoods, Gavryushkina FBD stratigraphic tip-dating priors, and Felsenstein Phylogenetic Independent Contrasts (PIC) + Ornstein-Uhlenbeck tree imputation.

🔗 Pipeline Integrated & Before/After Impact: DAG: gotoh-msa → felsenstein-modeltest → mk-morpho-tip-dating → bionj-nni-ml-tree → quartet-msc-coalescent
Before: Polyphyletic Caninae crown (RF = 0.34); R² = 0.61 non-PIC C-value regression.
After: 100.0% Caninae clade concordance (LPP = 0.99, RF = 0.028, 28.4× speedup) & R² = 0.934 GoaT C-value imputation.

RN-2026-001 • v1.0.0 🚀 Core Engine Architecture Launch runie (src/runie.rs • candle-core + rayon GA-MCMC)

Oct 31, 2026 • 23-Operator Markov DAG State Space

Launch of RuNIE: 4-Generation Step-Up Inference, Minimum Knowledge Gate (K_min) & Dev/Reserve Parameter Freeze

⚠️ Problem / Blind Spot Identified: Hardcoded single-modality scripts fail silently when biological datasets violate tool assumptions, and tuning parameters on the evaluation cohort causes severe benchmark overfitting.

🛠️ Solution & Architecture Deployed: Built RuNIE on pure-Rust candle-core tensors and rayon 4-chain parallel-tempering GA-MCMC (β ∈ {0.25, 0.50, 0.75, 1.00}), enforcing the 4-Generation Step-Up loop and strict Development-to-Untouched-Reserve parameter freezes.

🔗 Pipeline Integrated & Before/After Impact: Scope: 9 canonical multi-modal studies + Tool Validation #16.
Before: Single-tool exploratory baselines (mean P_posterior < 0.02).
After: 10/10 converged MAP pipelines (mean P_MAP = 0.90, mean ln BF₁₀ = +164.7 nats, 18 0🧪 rejects filtered).

Command	Domain	Status	What It Analyzes & External Counterpart	Key Output & Concordance Metric
`align-compare`	Tool Benchmark #1	✅ Validated	Native Rust aligner (codon + Gotoh affine-gap) vs. `MAFFT v7.526`	100% coding column agreement; 0.9963 overall rRNA/COI score; 4.82× speedup
`modeltest-compare`	Tool Benchmark #2	✅ Validated	Native 24-model Felsenstein pruning engine vs. `jModelTest v2.1.9`	r = 0.9999998 log-likelihood; 100% BIC/AICc agreement; 14.3× speedup
`tree-compare`	Tool Benchmark #3	✅ Validated	Native 4-stage BIONJ + pulley NNI ML tree builder vs. `IQ-TREE v2.4.0`	54-taxon vertebrate ML topology (RF = 0.0392, 98.04% splits); 8.41× speedup
`coalescent-compare`	Tool Benchmark #4	✅ Validated	Native quartet multispecies coalescent & ABBA-BABA vs. `ASTRAL v5.7.8`	1,064 gene trees (RF = 0.0000); r = 0.9999994 quartet support; 9.18× speedup
`selection-compare`	Tool Benchmark #5	✅ Validated	Native 61/60-state Goldman-Yang codon CTMC & 4D Grid BEB vs. `PAML v4.10.10` (`codeml`)	r = 0.9999982 lnL; r = 0.99994 ω₀; 100% BEB site F1; 9.42× speedup
`orthology-compare`	Tool Benchmark #6	✅ Validated	Native Smith-Waterman BLOSUM62, Emms-Kelly length normalization & RBH vs. `DIAMOND v2.2.8`	r = 0.99984 bit-score; 100% RBH 1:1 ortholog F1; +42.9% twilight recall
`synteny-compare`	Tool Benchmark #7	✅ Validated	Native double-stranded (w, k)-minimizer, concave-gap chaining & SV caller vs. `Minimap2 v2.31`	100% syntenic block & SV recall; r = 0.99991 divergence (`de`); 3.12× speedup
`gene-compare`	Tool Benchmark #8	✅ Validated	Native 4-stage 6-frame ORF graph, dicodon hexamer Markov & 28-bin Shine-Dalgarno RBS EM trainer vs. `Prodigal v2.6.3`	100% 3′ stop; 99.1% exact 5′ TIS; r = 0.9989 `cscore`; 5.84× speedup
`hmm-compare`	Tool Benchmark #9	✅ Validated	Native 4-stage Plan-7 Profile HMM engine (`p7_GMSV`, `p7_GViterbi`, `p7_GForward/Backward`, `p7_GOptimalAccuracy` & `p7_GNull2`) vs. `HMMER v3.4`	100% domain F1; r = 0.9999984 bit-score (0.042 bits MAE); 1.72 bp boundary error
`nonb-dna-compare`	Tool Benchmark #10	✅ Validated	Native G4/i-motif scorer & exact 65,536-state Z-DNA dinucleotide Boltzmann engine vs. `G4Hunter` & `Z-Hunt-II`	r = 1.0000000 G4Hunter score; r = 0.9999994 log₁₀(P_Z); 100% hotspot F1; 14.2× speedup
`rna-fold-compare` / `na-1d2d3d-compare`	Tool Benchmark #11	✅ Validated	Native Turner 2004 / SantaLucia 1998 Zuker MFE & McCaskill partition function + 1D-to-3D folding vs. `ViennaRNA v2.7.2` & PDB	r = 0.999982 ΔG_MFE; 99.42% BP F1; 1.84 Å 3D backbone RMSD; 4.65× speedup
`pocket-dock-compare`	Tool Benchmark #12	✅ Validated	Native 3D α-sphere Voronoi cavity detector & 5-term Vina BFGS/MC docking engine vs. `fpocket v4.2.3` & `AutoDock Vina v1.2.7`	100% top-1 pocket & pose (≤ 2.0 Å); r = 0.9999998 ΔG_dock; 0.34 Å RMSD; 11.48× speedup
`pangenome-compare`	Tool Benchmark #13	✅ Validated	Native rGFA variation graph constructor, bubble decomposition & haplotype walk projection vs. `minigraph v0.21-r606` & `gfatools v0.5-r296`	100% rGFA segment/link/bubble F1; 0.46 bp SV error; 100% walk call concordance; 16.73× speedup
`amr-compare` & `hgt-scan`	Tool Benchmark #14	✅ Validated	Native 2,253-node Reference Gene Hierarchy (`fam.tsv`), point-mutation, porin-disruption & tetranucleotide D_KL HGT island engine vs. `NCBI AMRFinderPlus v4.2.7` (DB `2026-08-07.1`)	72/72 call match across 10 ESKAPE cohorts (Jaccard = 1.0000); 100% node & method concordance; 9.67× HGT D_KL separation
`bgc-compare` / `bgc-round4` / `bgc-detect`	Tool Benchmark #15	✅ Validated	Native 56-Pfam Plan-7 profile scan & architecture-rule BGC caller (`RuleSet::V4`) across 36 genomes (182.8 Mb) vs. `GECCO v0.11.0` & `MIBiG 4.0`	76/91 (83.5%) dev & 19/24 (79.2%) 2nd-reserve bacterial BGC recall (17/17 NRPS/PKS, p = 0.250); 1 vs. 35 false-positive clusters across 11 controls
`relax-compare` / `pseudo-loss`	Tool Benchmark #16	✅ Validated	RuNIE-upgraded 3-frame codon-to-AA frameshift/stop aligner, localized homopolymer repeat indel guard & 3-model branch selection relaxation (k) vs. `MACSE v2.07` & `PAML v4.10.10`	100% `!` & `*` F1 and 100% AA identity vs. MACSE v2.07; Branch ln L r = 1.0000, RELAX k MAE = 0.0033, and 12/12 (100%) classification match (6 Dev + 6 Reserve)
`runie` (6 Synthesized Domain Tools)	RuNIE Inference Engine	✅ Validated	Autonomous `candle-core` + `rayon` `GA-MCMC` Step-Up synthesizer (`mk-morpho-tip-dating`, `kaiabc-allosteric-oscillator`, `universal-rp16-supermatrix`, `se3-rfdiffusion-scaffolder`, `mrna-construct-optimizer`, `spidroin-biomechanics-regressor`)	9/9 canonical scientific studies solved across Tiers 1–3 (mean P_MAP = 0.8979, mean ln BF₁₀ = +164.67 nats, 18.5×–39.4× speedup)
`bgc-mine` / `antismash-compare`	Natural Products	🔬 In Validation (Future Tool)	Rule-based `antiSMASH v7.1` comparison, `MIBiG` dereplication & self-resistance target paralogs	PKS/NRPS/terpene synthase co-localization and duplicated housekeeping paralogs
`co-evo` / `dca-compare`	Co-Evolution & Epistasis	🔬 In Validation (Future Tool)	Potts direct-coupling analysis & APC-corrected mutual information vs. `plmDCA` / `GREMLIN` / `EVcouplings`	3D contact-map precision (L/5, L/2) and compensatory rRNA/protein pairs
`haplo-cluster` / `popgen-compare`	Population Genetics	🔬 In Validation (Future Tool)	Minimum spanning haplotype networks, F_ST & Tajima's D vs. `PopART` / `Arlequin v3.5` / `vcftools`	Exact MSN edge topology, nucleotide diversity (π), and demographic neutrality tests
`coi-barcode-cluster` / `abgd-compare`	Systematics & Barcoding	🔬 In Validation (Future Tool)	Automated barcode gap discovery & NUMT paralog filtering vs. `ABGD` / `ASAP` / `PTP` / `BOLD`	K2P/TN93 species partitions, barcoding gap ratios, and reading-frame NUMT rejection
`finemap-compare`	Statistical Genetics	🔬 In Validation (Future Tool)	Native Sum-of-Single-Effects (SuSiE IBSS) & Wakefield ABF fine-mapping vs. `SuSiE-R` / `FINEMAP v1.4`	Posterior Inclusion Probabilities (PIP) and 95% causal credible sets under LD
`mr-twas-compare`	Causal Genomics	🔬 In Validation (Future Tool)	Native Two-Sample Mendelian Randomization (IVW, Egger, Median) & colocalization vs. `TwoSampleMR` / `coloc v5`	Causal effect estimates (β_MR), pleiotropy intercepts, and PP.H4 colocalization
`splicing-crispr-compare`	RNA Splicing & Editing	🔬 In Validation (Future Tool)	Native MaxEnt 5′/3′ splice-site entropy & CFD off-target guide scorer vs. `MaxEntScan` / `SpliceAI` / `CRISPRoff`	Cryptic splice activation (ΔMaxEnt) and Cas9/ABE/CBE editing window efficiency
`assembly-compare`	Genome Assembly	🔬 In Validation (Future Tool)	Native De Bruijn / string graph unitigging & error-bubble popping vs. `SPAdes` / `Flye` / `hifiasm`	NG50 contiguity, BUSCO completeness, and assembly misjoin error rate
`kmer-complexity-compare`	Sequence Information	🔬 In Validation (Future Tool)	Native canonical k-mer counter, MinHash sketch & Lempel-Ziv complexity vs. `Jellyfish v2.3` / `Mash v2.3`	Exact k-mer spectrum histograms, Mash distance correlation, and throughput
`chrom-condensate` & `clonal-synth`	3D Chromatin & Somatic	🔬 In Validation (Future Tool)	Chromatin contact graphs, phase-separation IDR scoring & somatic signature deconvolution vs. `IUPred3` / `SigProfiler`	Fiedler algebraic connectivity (λ₂), COSMIC SBS weights, and clonal trees
`disease-atlas` & `sweep`	Clinical Panels & Calibration	🔬 In Validation (Future Tool)	630-gene 32-panel clinical pleiotropy index & symmetric 0🧪–5🧪 calibration sweeps vs. `ClinGen` / `PanelApp` / `OMIM`	Cross-panel pleiotropic hub entropy (H_pleio) and empirical null gate boundaries

Bioinformatics, Systematics & Emergent Genome Complexity

Lab Discoveries Journal

Bayesian Markov-Chain Pipeline Inference and Multi-Modal Replication Across Nine Canonical Genomic and Structural Benchmarks

Released Profiles, 56 Marker Families and Two-Stage Reserve-Genome Validation Against GECCO

Benchmarking a Domain-Architecture Rule Engine Against GECCO on Five Genomes with Curated MIBiG Loci

Hierarchical Antimicrobial Resistance, Porin Disruption & Mobile HGT Island Calibration: Benchmarking Against NCBI AMRFinderPlus

Native rGFA & Walk Entropy Engine vs. minigraph v0.21 & gfatools v0.5

Benchmarking Alpha-Sphere Druggability and SE(3) Empirical Scoring Against fpocket and AutoDock Vina

Benchmarking DNA & RNA Folding Against ViennaRNA, RNAPKplex, and US-align

Native Turner-2004 Zuker–McCaskill Engine vs. ViennaRNA (RNAfold v2.7.2)

Mapping Non-B DNA G-Quadruplexes and Left-Handed Z-DNA Supercoiling Hotspots (vs. G4Hunter & Z-Hunt-II)

Identifying Protein Functional Domains with Plan-7 Profile Hidden Markov Models (vs. HMMER v3.4)

Predicting Protein-Coding Genes and Ribosome Binding Sites Across GC Gradients (Dicodon Markov Models vs. Prodigal)

Mapping Whole-Genome Synteny, Chromosomal Inversions, and Genomic Islands (Minimizer Chaining vs. Minimap2)

Evaluating Statistical Significance vs. Sample Size Across 6.65 Mb of Genomes

Benchmarking Six Phylogenomic Stages from Protein Orthology to Species Trees

Separating Orthologs from Paralogs Across Divergent Genomes (RBH vs. DIAMOND)

Detecting Positive Selection in Protein-Coding Genes (Codon dN/dS vs. PAML)

Resolving Gene-Tree Conflict and Incomplete Lineage Sorting Across 1,064 Loci

Maximum-Likelihood Phylogenetic Tree Inference Across 55 Vertebrate Species

How Sequence Alignment Choices Affect DNA Substitution Model Selection

Selecting DNA Substitution Models Across Protein-Coding and Ribosomal Genes

Affine-Gap Multiple Sequence Alignment Across Coding and Ribosomal Loci

Resolving Bird Evolutionary Relationships with a Four-Gene Ribosomal Supermatrix

Ribosomal DNA Secondary Structure and Nuclear Pseudogene Filtering in 32 Bird Genomes

How the APOE Christchurch (R136S) Mutation Alters Protein Stability and Receptor Binding

G-Quadruplex DNA Structures and Variable Tandem Repeats at the Human APOE–TOMM40 Locus

Shared Genetic Pathways and DNA Repeat Architecture Across 630 Human Disease Genes

Species Identification Limits and Antibiotic Selectivity Across Ribosomal and Mitochondrial Genes

Tracking Mobile Antibiotic Resistance Plasmids and Mutational Constraints in Pathogenic Bacteria

Combining Chromatin Structure and Mammalian Gene Loss to Identify Candidate Drug Targets

Ribosomal DNA G-Quadruplexes and Subtelomeric Chromatin Organization Across Six Human Chromosomes

How Mobile Carbapenemase Resistance Islands Integrate at Bacterial tRNA Genes

Pairing Mitochondrial COX1 and 16S rRNA to Filter Out Nuclear Pseudogenes in Vertebrate Barcoding

Why Single-Copy rpoB and gyrB Genes Outperform 16S rRNA for Identifying Closely Related Bacteria

Why Aminoglycoside Antibiotics Target Bacterial Ribosomes and Trigger Mitochondrial Hearing Loss

Comparing Taxonomic Resolution Limits Across Bacterial and Eukaryotic DNA Barcode Markers

Combining Mitochondrial COI and 16S rRNA for Species Identification in Bony Fishes and Sharks

Distinguishing Close Bacterial Relatives and Foreign Resistance Islands in Enterobacteriaceae

Promoter CpG Islands and G-Quadruplex DNA Motifs at the Human ACTB–FSCN1 Locus

Distinguishing Antibiotic Biosynthetic Gene Clusters from Core Metabolic Genes in Bacteria

G-Quadruplex DNA Clustering at Human Chromosome Ends and 28S Ribosomal RNA Repeats

Comparing GC Content and Secondary Structure Evolution Across Bacterial, Mitochondrial, and Nuclear rRNAs

Co-Evolutionary Constraints Between Antibiotic Resistance Mutations in Bacterial Ribosomes and DNA Gyrase

How Genome GC Content Drives G-Quadruplex Density and Horizontal Gene Transfer Signals in Bacteria

Conserved Stem-Loop Structure and Compensatory Resistance Mutations in Ribosomal RNA

Using the Conserved 5.8S rRNA Core to Anchor Fungal ITS Species Barcoding

How Multiple 16S rRNA Gene Copies Within One Bacterial Genome Inflate Microbiome Diversity Counts

Visualizing Mitochondrial DNA Haplotype Networks in Bears (Ursus) and Tunas (Thunnus)

Distinguishing True Biological Signal from Background Sequence Noise Across Eight Genomic Datasets

Mitochondrial COI Barcoding and Third-Codon GC Shifts in Warm-Bodied Tunas and Sharks

G-Quadruplex and Z-DNA Repeat Hotspots Near the Ends of Five Human Chromosomes

Natural Gene Loss in Diving and Hibernating Mammals Points to Safe Human Metabolic Drug Targets

Structural Variation and Alternative Splicing Across Six Medically Important Human Gene Loci

Tracking Sub-Clonal Tumor Mutations and Synthetic-Lethal Gene Pairs in Single-Cell Cancer Data

How Non-Coding RNA Methylation and Chromatin Looping Regulate Gene Expression on Human Chromosome 1p36

Compensatory Mutations and Fitness Trade-Offs in Bacterial NDM-1 Carbapenemase and DNA Gyrase

How an Intronic Tandem Repeat Controls Alternative Splicing in the Human CACNA1C Calcium Channel

Relaxed Natural Selection and Pseudogene Formation in Mammalian Metabolic Genes

Using Duplicated Housekeeping Genes to Locate Antibiotic Gene Clusters in Streptomyces

Detecting a Horizontally Transferred blaNDM-1 Carbapenemase Island in Pseudomonas aeruginosa

Mitochondrial COI DNA Barcoding and Codon Conservation Across 16 Carnivora Species

Mapping G-Quadruplex and Left-Handed Z-DNA Motifs in the Human AGRN Gene on Chromosome 1p36