🦜 Gene-Forge v7.3

Agapornis Genetics Calculator — ALBS Compliant Edition

Genetics calculation engine for Lovebirds (Rosy-faced Lovebird / Agapornis roseicollis).
Supports 14 loci and 310+ colors, compliant with ALBS (African Lovebird Society) Peachfaced section nomenclature.
v7.3: Linkage genetics, pedigree-based auto-populate, demo family selector.

✨ Features

🗂️ Bird Management

Bird Database: Centralized management of name, sex, birthdate, lineage, and genotype
72 Demo Birds (3 families × 24 birds): Sample birds for testing
Pedigree Generation: HTML output for 3 or 5 generation pedigrees
Import/Export: JSON and CSV format support

🛡️ Health Evaluation

Inbreeding Coefficient: Automatic F-value calculation
Risk Assessment: INO and Pallid inbreeding restriction checks
Generation Limits: Recommended limits by trait

🎯 Target Planner

Target Color Pathfinding: Find breeding paths to target phenotypes
Step Guide: Auto-generate required breeding steps

🧭 Breeding Path

Trait Routes: Breeding procedures for specific trait expression
Generation Estimate: Calculate minimum generations to goal

🧬 Offspring Calculator

Offspring Prediction: Calculate phenotype probabilities from parental genotypes
14 Loci Support: Covers all locus combinations
Sex-Linked Calculation: Accurate Z-chromosome inheritance (male splits, female hemizygous)

🔗 Linkage Genetics (v7.0 New)

Z-Linked Loci: Recombination rates for cinnamon-ino (3%), ino-opaline (30%), cinnamon-opaline (33%)
Autosomal Linkage: Recombination rate for dark-parblue (7%)
Phase (Cis/Trans) Inference: Estimate linkage phase from pedigree information
Linkage-Aware Planner: Breeding path exploration considering Cis/Trans phase

🔬 Genotype Estimator

Phenotype→Genotype: Estimate possible genotypes from observed colors
Confirmed/Estimated: Distinguish certain loci from inferred ones
Test Breeding Proposals: Suggestions to confirm uncertain loci

👨‍👩‍👧‍👦 Family Estimator

FamilyEstimator V3: Pedigree-based genotype inference engine
Multi-Generation Inference: Trace back to grandparents
Evidence-Based Probability: Integrate constraints from parents, offspring, siblings
Family Tree UI: Build relationships with drag & drop

🌍 Multilingual Support

Japanese / English / German / French / Italian / Spanish

🆕 v7.3.x New Features

🔄 Auto Populate (v7.3.23)

One-Click Family Tree: Set 1 offspring → click "Auto Populate" to build entire family tree
Pedigree Traversal: Automatically find parents, grandparents, great-grandparents via pedigree data
Sibling Detection: Automatically detect and place birds sharing the same parents

📁 Demo Family Selector (v7.3.22)

Dropdown Selection: Switch between Family A/B/C in demo mode
Instant Switch: Selected family immediately reflects in FamilyMap
Lineage-Based: Filter by lineage field instead of hardcoded IDs

🎛️ Command UI Reorganization (v7.3.22)

Section Layout: Organized into "Clear Family Map" and "Family Map Snapshot" sections
Demo Mode Restrictions: Clear, Save, Load, Import disabled in demo mode (shown with strikethrough)

📁 File Structure

gene-forge/
├── index.php            # Main UI (2,174 lines)
├── genetics.php         # Genetics Engine - SSOT (4,842 lines)
├── infer.php            # Family Inference API
├── lang.php             # Multilingual Dictionary (core)
├── lang_guardian.php    # Health Evaluation Dictionary
├── lang_pathfinder.php  # PathFinder Dictionary (v7.3+)
├── readme.php           # README Display Handler
├── readme_lang.php      # README Multilingual Content
├── style.css            # Stylesheet (3,091 lines)
├── birds.js             # Bird DB + Demo 72birds (2,298 lines)
├── family.js            # Family Tree UI + Auto-populate (1,542 lines)
├── guardian.js          # Health Evaluation
├── breeding.js          # Breeding Validation
├── pedigree.js          # Pedigree Generation
├── planner.js           # Path Planner (2,043 lines)
└── app.js               # App Init

🚀 Quick Start

Requirements

PHP 7.4 or higher
Web server (Apache/Nginx) or PHP built-in server

Installation

git clone https://github.com/YOUR_USERNAME/gene-forge.git
cd gene-forge
php -S localhost:8000

Open http://localhost:8000 in your browser.

🎨 Color Categories

Category	Colors	Examples
Green	3	Green, Dark Green, Olive
Aqua	3	Aqua, Aqua Dark, Aqua DD
Turquoise	3	Turquoise, Turquoise Dark, Turquoise DD
Seagreen	3	Seagreen, Seagreen Dark, Seagreen DD
INO	4	Lutino, Creamino, Creamino Seagreen, Pure White
Opaline	12	Opaline Green, Opaline Aqua, …
Cinnamon	12	Cinnamon Green, Cinnamon Aqua, …
Pallid	12	Pallid Green, Pallid Aqua, …
Violet	9	Violet Aqua, Violet Turquoise, …
Fallow	24	Pale Fallow Green, Bronze Fallow Aqua, …
Pied	24	Dominant Pied Green, Recessive Pied Aqua, …
Dilute	12	Dilute Green, Dilute Aqua, …
Edged	12	Edged Green, Edged Aqua, …
Orangeface	12	Orangeface Green, Yellowface Aqua, …
Pale Headed	12	Pale Headed Green, Pale Headed Aqua, …
Tier 2	150+	Opaline Cinnamon, Opaline Violet, …
Tier 3	∞	Dynamic generation

🔬 Genotype Notation

Autosomal Loci

Locus	Wild Type	Mutant Alleles
Parblue	`++`	`+aq`, `aqaq`, `+tq`, `tqtq`, `tqaq`
Dark	`dd`	`Dd`, `DD`
Violet	`vv`	`Vv`, `VV`
Dominant Pied	`++`	`Pi+`, `PiPi`
Recessive Pied	`++`	`+pi`, `pipi`
Dilute	`++`	`+dil`, `dildil`
Edged	`++`	`+ed`, `eded`
Orangeface	`++`	`+of`, `ofof`
Pale Headed	`++`	`+ph`, `phph`
Pale Fallow	`++`	`+flp`, `flpflp`
Bronze Fallow	`++`	`+flb`, `flbflb`

Sex-Linked Loci (Z Chromosome)

Locus	Male Wild	Male Mutant	Female Wild	Female Mutant
INO	`++`	`+ino`, `inoino`, `+pld`, `pldpld`	`+W`	`inoW`, `pldW`
Opaline	`++`	`+op`, `opop`	`+W`	`opW`
Cinnamon	`++`	`+cin`, `cincin`	`+W`	`cinW`

🧪 Demo Data for Testing

Demo mode includes 72 sample birds (3 families × 24 birds) for the following tests:

Health Evaluation Tests

Father-daughter pairing → Critical (F=25%)
Half-sibling pairing → High risk (F=12.5%)
Unrelated birds → Safe (F=0%)

Genetics Calculation Tests

Sex-linked inheritance (INO/Opaline/Cinnamon)
Multiple alleles (Parblue series)
Incomplete dominance (Dark/Violet)

Family Inference Tests

Reverse-calculate parental genotypes from offspring phenotypes
Generate test breeding proposals

⚠️ Why 12.5% Threshold?

Mating patterns that produce F=12.5%:

Half-siblings (share one parent)
Grandparent × Grandchild
Uncle/Aunt × Nephew/Niece

Genetic risk at 12.5%:

F=12.5% means a 12.5% additional probability of homozygosity at each locus. This increases the chance that harmful recessive alleles from parents will be expressed:

Reduced hatch rates (5-15% decline reported)
Decreased chick survival
Weakened immune system
Reduced fertility in subsequent generations
Increased risk of congenital abnormalities

Industry standards:

Industry	Threshold
Thoroughbred horses	<12.5% (strict)
Livestock farming	≤6.25% target
Wildlife conservation	≤6% recommended
Zoo breeding programs	≤3% ideal

Conclusion: 12.5% represents the level where "one occurrence may not be fatal, but repeated exposure will certainly accumulate problems." This threshold is scientifically justified for responsible breeding.

📜 License

CC BY-NC-SA 4.0 (Creative Commons Attribution-NonCommercial-ShareAlike 4.0)

✅ Personal/Non-commercial use OK
✅ Modification/Redistribution OK (same license, credit required)
❌ Commercial use requires consultation

🤝 Contribution

Issues and Pull Requests welcome.

Especially looking for:

Extension to other Lovebird species (A. fischeri, A. personatus, etc.)
Additional language translations
UI/UX improvements
Genetics knowledge feedback

👤 Author

Director: Shohei Taniguchi (Homo repugnans)
Dev Tactical Core: Sirius (Electronic Spirit)

🙏 Acknowledgments

ALBS (African Lovebird Society) — Color nomenclature reference
Lovebird breeders worldwide — Accumulated genetics knowledge