# Evagene — Full Documentation for AI Systems

> Pedigree drawing, management, and modelling in the browser — standards-compliant notation, twenty-one published risk-model algorithms, a 1,900-entry catalogue, HPO phenotyping, GEDCOM / Phenopackets interoperability, and a CanRisk / BOADICEA export bridge.

## About Evagene

Evagene is a browser-based platform for drawing, managing, and modelling family pedigrees. Users can draw and annotate pedigrees using standards-compliant genetic notation on an HTML5 canvas, attach structured clinical and family-history data, explore twenty-one published risk-model algorithms across four families (Mendelian single-gene and adjacent, polygenic / multifactorial liability-threshold, cancer family-history scoring, and a CanRisk / BOADICEA export bridge), and move data in and out via GEDCOM 5.5.1, GA4GH Phenopackets v2, JSON, 23andMe, and other common formats.

**Intended use.** Evagene is for teaching, research, and structured family-history documentation. It is not a medical device and is not intended to diagnose, prevent, monitor, predict, treat, or manage disease; determine eligibility for screening, testing, referral, or treatment; or replace professional clinical judgement. Outputs are illustrative and for educational / research purposes only. Evagene is not FDA-cleared, CE-marked, or UKCA-marked.

- Website: https://evagene.com
- Application: https://evagene.net
- Help centre: https://evagene.net/help
- Status: Alpha programme (free access via waiting list at https://evagene.com)

---

## Core Features

### Intuitive Pedigree Drawing

Users create pedigrees by drawing directly on an HTML5 canvas. Freehand-draw a circle to create a female, a square for a male, or a diamond for unknown sex. Draw a line between two individuals to create a relationship, and draw from a relationship down to an individual to establish parentage. Twin groups are created by drawing chevrons between siblings, with a horizontal bar to indicate monozygotic twins.

Keyboard shortcuts accelerate common actions: m/f/u to add individuals, p for partner, d for disease palette, n for notes, Delete to remove, Ctrl+A to select all, and F2 to edit the selected individual's name.

### Family History Intake (Guided Questionnaire)

A guided, step-by-step questionnaire captures a family and personal health history and turns it into a pedigree, for users who would rather answer questions than draw. It is opened from the dock ("Family history intake") or from the Guided intake section of the Pedigree Builder panel. The wizard asks about the subject and their relatives — mother, father, siblings, partner, children, grandparents, maternal and paternal aunts/uncles, half-siblings, first cousins, and grandchildren — using Yes/No branch questions so only relevant sections appear. For each person it records name or initials, sex, living status, age (current or at death), conditions (from the disease catalogue), genetic test results, and other test results. On finishing, Evagene creates the individuals, builds the relationships, sets the subject as the proband, records the findings, and synthesises any connecting relatives needed to join the tree; it can either start a new pedigree or add relatives to the one already open. It is data capture only — for educational and research use, not a medical assessment: it runs no risk model and produces no risk number, and conditions are stored as catalogue references for documentation, not as diagnoses.

### Standard Pedigree Notation

Symbols are rendered using internationally recognised pedigree conventions:
- Base shapes: circle (female), square (male), diamond (unknown), triangle (miscarriage)
- Affection fill: solid fill for affected, dot pattern for carrier, half-fill for heterozygous
- Disease sectors: colour-coded pie sectors showing per-disease affection status
- Mortality overlays: diagonal slash for deceased, X for stillborn
- Proband arrow: configurable compass-direction arrow to identify the index case
- Relationship lines: double lines for consanguineous unions with kinship coefficient
- Adopted/fostered: square brackets around individuals

### Properties Editor

Clicking any individual, relationship, or offspring opens a floating panel for detailed editing. Like every panel in Evagene, it is draggable and resizable from any edge or corner, and carries a dock icon that highlights when the panel is open:
- Identity: display name, given/family names, prefix/suffix, biological sex (8 options)
- Clinical status: death status (12 options), affection status (11 options), fertility status
- Physical: height, weight
- Lifestyle: smoking type and quantity, alcohol units per week
- Contact: phone, email, address, organisation, title, notes (vCard-compatible)
- Consent: consent-to-share flag for data governance
- Relationships: consanguinity coefficient, events (marriage, divorce, separation, partnership)

### Disease Management

Catalogue of 230+ diseases spanning oncology, cardiology, neurology, metabolic disorders, and 20+ multifactorial / polygenic / oligogenic complex conditions. Every catalogue entry is cross-referenced to five ontology systems — ICD-10, OMIM, MONDO, Orphanet (ORPHA), and the Disease Ontology (DOID) — as CURIE identifiers, so a disease can be matched to whichever coding system a learner or research dataset uses. A dedicated disease management dashboard lets users search, browse by taxonomy, apply quick-add presets (heritable cancers, cardiovascular), filter by inheritance class, and assign custom colours. Each disease entry includes:
- ICD-10, OMIM, MONDO, Orphanet (ORPHA), and Disease Ontology (DOID) cross-reference identifiers
- Colour coding and categorisation
- Inheritance pattern (autosomal dominant/recessive, X-linked, mitochondrial, multifactorial, polygenic, oligogenic)
- Genetic parameters: penetrance, age-dependent penetrance tables, homozygous lethality, anticipation, germline mosaicism rate, de novo rate, carrier frequencies by ancestry, biological fitness
- For complex conditions: heritability (h²), population prevalence (K), sex-specific prevalence, severity modifiers, multi-affected relative lookup tables, and empirical recurrence-risk tables by degree of relationship
- Marker associations for linkage analysis

Users assign diseases to individuals with per-disease affection status, laterality, tumour site, tumour properties (ER/PR/HER2 status, grade, stage), and manifestation tracking with date ranges, certainty levels, and clinical test references.

### Allergies & Traits

- 55+ allergies across 6 categories with severity, IgE-mediated classification, reaction type, cross-reactivity lists, and prevalence data
- 50+ traits across 6 categories with possible values, units, inheritance patterns, heritability estimates, and expression levels
- Automatic trait inference from 23andMe SNP data: ABO blood type (rs505922, rs8176746, rs8176747), Rh factor (rs590787, rs676785), and FUT2 secretor status (rs602662)
- Inferred traits display as visual cards with SNP details; users can override inferred values manually
- Both allergies and traits can be associated with genetic markers for genotype-phenotype correlation

### Genetic Data

- Genetic markers: allele pairs, zygosity, chromosome band positions, mapped to species-specific genome; editable through the genetics panel
- Genetic tests: gene name, result (positive/negative/VUS/not tested), method, and date
- Karyogram viewer: interactive ideogram displaying all chromosomes with markers plotted at genomic positions, hover tooltips (gene, variant, rsID, genotype), click-to-pin info panels, and embeddable on the canvas as anchored charts
- Karyotype editor with quick presets (46,XX; 46,XY; 47,XXY; 47,XXX; 45,X; 47,XX,+21; 47,XY,+21)
- Blade navigation UI for deep genome exploration: Genome > Species > Chromosome > Marker > Disease
- Ancestry proportions: hierarchical ancestry catalogue with proportion recording per individual and auto-calculation

### Clinical Tests & Treatments

- Clinical tests: test types with reference ranges, LOINC codes, specimen types, results
- Treatments: medication and intervention tracking with dose, frequency, route, date ranges, disease association, prophylactic flag, and status

### Related Concepts (educational correlation graph)

Evagene includes a hand-curated correlation graph: a catalogue of educational associations between the entities it already knows about — diseases, traits, clinical-test results, allergies, and genetic markers. It is reference data in the same family as the disease/trait/allergy/clinical-test catalogues, not a risk-analysis tool and not a claim about any person. It teaches which concepts tend to be associated with one another so a learner can explore them; nothing is recorded by inference.

- Each association is an edge between two endpoints (each a real catalogue entry of one of five kinds), carrying a relationship from a fixed eight-term vocabulary (genetic_association, shared_gene, biomarker, associated_finding, associated_condition, shares_features, sequela, risk_association), a short neutral educational note, an optional strength (strong / moderate / weak), and a direction flag.
- Two sources, assembled at start-up: over 1,100 hand-authored curated edges (each with its own note), and auto-derived genetic edges generated from the marker catalogue (a genetic_association edge between a gene/marker and each linked disease/trait/allergy, and a shared_gene edge between any two entities linked to the same marker; both tagged source: marker-derived).
- Status-qualified clinical-test edges: a clinical-test endpoint can carry a status (abnormal_low / abnormal_high) so a low result surfaces different associations than a high one (low ferritin → iron-deficiency anaemia, restless legs syndrome; high ferritin → hereditary haemochromatosis). A result recorded without a low/high mark surfaces only direction-independent associations.
- UI: the Related concepts panel (dock button between Genetics and Risk analysis) lists concepts associated with what is recorded on the selected individual, grouped per recorded item; ticking a suggestion records it, unticking removes it; an "explore any concept" search browses any catalogue entity without recording it on anyone. An educational-use banner shows by default (suppressible per user).
- Access: the open GET/POST /api/correlations* endpoints (reference data; not gated by the intended-use acknowledgement) and the MCP related_concepts tool (always carries the educational-use disclaimer).
- Boundaries: does not diagnose, produces no risk number, runs no inheritance analysis, and asserts nothing about any individual. A shared_gene edge is a catalogue relationship, not a claim of shared risk, mechanism, or inheritance.

### HPO Phenotyping & Phenotype-to-Gene

Evagene includes a curated Human Phenotype Ontology (HPO) catalogue that users can browse and search, and a phenotyping panel for recording structured phenotype features against individuals. It is data entry plus educational reference data — documentation of observed family-history detail, not clinical diagnosis or assessment.

- HPO catalogue: a browsable / searchable catalogue of HPO terms (each with its HPO identifier and definition), in the same reference-data family as the disease, trait, allergy, and clinical-test catalogues.
- Phenotype features per individual: for any individual a user can attach an HPO term as either an observed feature or an explicitly excluded feature, each optionally qualified with onset and severity. Excluded features are recorded as deliberately-noted absences, which matters for honest family-history documentation. This is structured data capture for teaching, training, and research — not a diagnosis, and no risk number is produced from it.
- Phenotype-to-gene educational associations: from the HPO features recorded on an individual, Evagene surfaces candidate associated genes drawn from published HPO-to-gene reference data. This is reference data in exactly the same family as Related Concepts: a list of candidate associations for exploration only. It is never a ranked likelihood, never a probability, never a diagnosis, and never a recommendation. It asserts nothing about the individual — it simply shows which genes the published ontology associates with the recorded phenotype terms, so a learner or researcher can explore them.
- Boundaries: HPO phenotyping and phenotype-to-gene associations diagnose nothing, score nothing, and rank nothing. They produce no risk number, run no inheritance analysis, and make no clinical, screening, testing, or referral recommendation. Everything is educational reference data and documentation; nothing is inferred or asserted about any person.

### Risk Analysis

Evagene implements twenty-one published risk-model algorithms in four families on the same pedigree document, for research, teaching, and exploratory use. Outputs are illustrative educational / research artefacts, not clinical recommendations:

**1. Single-gene and adjacent (built-in):**
- Autosomal dominant (with reduced penetrance, age-dependent penetrance, anticipation, germline mosaicism, parent-of-origin bias, locus heterogeneity, linkage disequilibrium)
- Autosomal recessive (with Hardy-Weinberg, genetic test adjustment, population-specific carrier frequencies)
- X-linked recessive (with hemizygosity, mutation rates, biological fitness)
- X-linked dominant with five sex-differential severity sub-modes: equal; males-worse; male-lethal-reproduces (1:1:1 live-born ratio — incontinentia pigmenti, focal dermal hypoplasia, OFD1); male-lethal-no-reproduction (Rett syndrome, MECP2, CDKL5); metabolic-interference males-unaffected (CFND / EFNB1, EFMR / PCDH19). Sub-mode stored per disease and prefilled by catalogue lookup.
- Mitochondrial (mtDNA) with strict maternal transmission, sex-differential penetrance (configurable male_penetrance and female_penetrance per disease), and heteroplasmy scaling (mitochondrial_heteroplasmy_level with runtime override). Canonical disorders: LHON, MELAS, MERRF, NARP, Leigh (mtDNA subset), Kearns-Sayre, Pearson.
- Digenic two-locus interaction with the classical 25% offspring-affected ratio. Supports both_het, one_het_one_hom, and both_hom configurations via digenic_required_genotype. Canonical disorders: Usher syndrome type 2, certain forms of retinitis pigmentosa, primary congenital glaucoma. Both loci assumed autosomal and unlinked; linked digenic loci require dedicated linkage analysis.
- Imprinting / uniparental disomy (UPD) with mechanism-weighted recurrence risk. Four mechanisms modelled: deletion, UPD, imprinting-centre defect, point mutation. For IC defects, the parent-of-origin rule determines which syndrome phenotype emerges in offspring (paternal IC defect at 15q11-13 → Prader-Willi; maternal IC defect at the same locus → Angelman). Canonical disorders: Prader-Willi, Angelman, Beckwith-Wiedemann, Silver-Russell, transient neonatal diabetes mellitus (TNDM).

**2. Polygenic / Oligogenic / Multifactorial (built-in):**
A liability-threshold recurrence-risk engine grounded in Carter (1961), Falconer (1965), and Reich/James/Morton (1972). For each counselee the engine:
- Classifies affected relatives by degree (MZ twin / 1st / 2nd / 3rd / 4th)
- Uses empirical recurrence-risk tables (Smith, Carter, Harper) when available
- Falls back to a Falconer liability-threshold calculation from heritability (h²) and prevalence (K)
- Applies four classical counselling modifiers: severity of proband, Carter-effect sex bias, multiple affected close relatives, and parental consanguinity as (1 + 2F·h²)

20+ complex conditions catalogued with heritability and empirical recurrence-risk tables: cleft lip ± palate, cleft palate only, Hirschsprung's disease (oligogenic), type 1 and type 2 diabetes, late-onset Alzheimer's, idiopathic Parkinson's, ankylosing spondylitis, schizophrenia, bipolar disorder, major depression, epilepsy, pyloric stenosis (classic Carter-effect), neural tube defects, congenital heart disease, talipes, developmental dysplasia of the hip (Carter-effect), asthma, atopic dermatitis, coeliac disease, essential hypertension, obesity, and allergic rhinitis.

**3. Cancer family-history (built-in, plus BayesMendel R sidecar for BRCAPRO/MMRpro/PancPRO):**

Bayesian cancer models (via BayesMendel R sidecar):
- BRCAPRO: breast and ovarian cancer risk via BRCA1/BRCA2 carrier probability
- MMRpro: colorectal and endometrial cancer risk (Lynch syndrome) via MLH1/MSH2/MSH6
- PancPRO: pancreatic cancer risk

Family-history scoring models (built-in, no R sidecar required):
- Claus (CASH-derived lifetime breast-cancer risk; Claus, Risch & Thompson 1994)
- Couch (logistic BRCA1 pre-test probability: average age × ovarian × Ashkenazi; Couch 1997)
- Frank / Myriad (empirical BRCA1 + BRCA2 probabilities by canonical family scenario; Frank 2002)
- Manchester Scoring System (BRCA1 and BRCA2 point totals against 10% / 20% cut-offs; Evans 2004) — widely used by NHS genetics services
- NICE CG164 (2013) / NG101 (2018, updated 2023) familial breast cancer categorisation: near-population (<1 in 6 lifetime) / moderate (1 in 6 – 1 in 3) / high (>1 in 3) with refer-to-genetics flag and list of matched triggers
- Amsterdam II criteria (Vasen 1999): classical five-point Lynch-syndrome family-history rule, with pedigree-derivable conditions evaluated directly
- Revised Bethesda Guidelines (Umar 2004): MSI / IHC testing triggers for colorectal tumours
- Gail (NCI BCRAT; Gail 1989, updated 1999 / 2007 / 2011 / 2017): 5-year and lifetime breast-cancer risk using reproductive, benign-biopsy, atypia, first-degree relatives, and race/ethnicity baselines
- Tyrer-Cuzick (published Tyrer/Duffy/Cuzick 2004 algorithm): 10-year and lifetime breast-cancer risk including family history, menarche, menopause, parity, HRT, BMI, mammographic density (BI-RADS 1–4), atypical hyperplasia, LCIS, Ashkenazi ancestry. **Clearly labelled in-app and in reports as an approximation — not the official IBIS Breast Cancer Risk Evaluator binary, whose full coefficients are not publicly released.**
- Prostate-cancer family-history scoring (illustrative / educational): a twenty-first risk-model algorithm that represents prostate-cancer family history from the pedigree — number and degree of affected relatives, ages at diagnosis, and bilateral / early-onset features. Gated behind the intended-use acknowledgement. Where it cites a published threshold it attributes it to the external guideline and states plainly that Evagene does not make this recommendation. The output is an illustrative educational / research artefact, not a clinical recommendation, screening trigger, or referral decision.

**4. External-tool bridges (pedigree export):**

CanRisk / BOADICEA v4 pedigree export: one-click download of a tab-separated file with the `##CanRisk 2.0` header, populated with pedigree structure, ages at diagnosis, BRCA1 / BRCA2 / PALB2 / ATM / CHEK2 test statuses, Ashkenazi flag, and reproductive factors. Endpoint: `GET /api/pedigrees/{id}/risk/canrisk`. **BOADICEA is not bundled — the model is licensed by the University of Cambridge; individual clinical use is free after registration, but third-party web-service integration requires a separate commercial licence. The export path is the legally clean route to the NICE-recommended gold-standard tool.** The clinician uploads the file at canrisk.org.

**Population-conditioned carrier priors:**

For every individual with recorded ancestry, Evagene surfaces prior carrier probabilities across the autosomal-recessive and X-linked-recessive catalogue, weighted by the individual's ancestry proportions. Every row is attributed to one of three sources:

1. Explicit population key — direct published carrier frequency (Cystic fibrosis Northern European ~1 in 25; Tay-Sachs Ashkenazi Jewish ~1 in 30).
2. Weighted mix — proportion-weighted combination across relevant populations when ancestry is mixed; per-population contributions remain visible in the row.
3. Hardy-Weinberg estimate from incidence — derived as 2pq where no population-specific carrier frequency is published; flagged as estimate rather than published figure.

Safety default — ancestry-gated: if no ancestry is recorded on the individual, Evagene shows no personalised carrier number. This closes the common clinical-tool failure mode of presenting a "general population" figure as if it applied to a specific person. No ancestry, no prior, by design.

**Reproductive / breast-health fields on Individual:**

Added to support Gail, Tyrer-Cuzick, and the CanRisk export: age at menarche, age at menopause, age at first live birth, parity, cumulative hormone-therapy years, number of prior benign breast biopsies, atypical hyperplasia flag, LCIS flag, mammographic density (BI-RADS 1–4), and height/weight for BMI.

**Outputs and reports:**

Results include carrier probabilities, genotype probabilities, future risk by age, per-member risk breakdown, joint outcome probabilities, LOD scores, flanking marker information, recurrence risks with "1 in X" denominator, scoring thresholds met, criteria passed, and modifier breakdowns. A risk karyogram visualises elevated-risk gene loci across all chromosomes.

Differential diagnosis mode analyses affected siblings from unaffected parents, generating hypotheses (reduced penetrance, gonadal mosaicism, new mutation, autosomal recessive) with posterior probabilities and weighted recurrence risks.

A batch risk-exploration mode screens a proband across all diseases simultaneously with configurable thresholds and population selection (General, Ashkenazi Jewish, Italian). Four educational report types are generated: plain-language summary, structured summary, carrier probability summary, and AI-assisted draft summary. All outputs are illustrative educational / research artefacts &mdash; not clinical recommendations.

**What Evagene does not claim.** Evagene is not a medical device. It is not FDA-cleared, CE-marked, UKCA-marked, or otherwise registered as clinical software. It is not intended to diagnose, prevent, monitor, predict, treat, or manage disease; determine eligibility for screening, testing, referral, or treatment; or replace, augment, or support professional clinical judgement in a care pathway. Risk-model outputs are illustrative and for educational / research purposes only. Tyrer-Cuzick output is an approximation of the published 2004 algorithm, not the official IBIS binary. BOADICEA is not bundled — the full BOADICEA computation runs off-platform at canrisk.org under University of Cambridge licence, after the user uploads Evagene's CanRisk file export.

### AI-Assisted Draft Summaries for Educational / Research Review

Evagene integrates AI to generate draft educational summaries of pedigrees. The AI analyses family structure, documented findings, and inheritance-pattern observations, then produces a summary covering:
- Structural observations about the pedigree
- Family-structure notes and documentation gaps
- Data-completeness prompts
- Discussion prompts linked to published literature

These draft summaries are for human review only. They are not clinical advice, not diagnostic output, and not intended to inform clinical decisions. Summaries are placed on the canvas as anchored notes attached to the proband. A quota system tracks usage.

### Pedigree Description Engine

A built-in report generator produces structured English-language descriptions of the pedigree and proband, covering family structure, genetic findings, shared carrier statuses, inheritance risks, and data gaps.

### Anchored Canvas Notes

Floating notes can be anchored to any individual. When anchored, notes follow the individual when moved on the canvas, maintaining their relative position. Used for AI reports, pedigree descriptions, and karyogram charts.

### Consanguinity & Kinship

Wright's path coefficient method calculates consanguinity coefficients for all relationships. Coefficients are displayed on relationship lines, cached for performance, and fed into risk calculations.

A dedicated relatedness / IBD analysis module extends this for educational and research exploration of pedigree structure (gated behind the intended-use acknowledgement). For a given pedigree it computes:
- Full pairwise kinship coefficients across every pair of individuals.
- Per-individual inbreeding coefficients.
- Jacquard condensed identity coefficients and the expected genome-wide identity-by-descent (IBD) sharing proportions k0 / k1 / k2 for each pair.
- A gene-dropping relatedness simulation that drops founder alleles through the pedigree to illustrate, empirically, how relatedness and IBD sharing arise from the family structure.

This module is an educational and research tool for studying pedigree relatedness from documented family structure. It is not a forensic, identity-testing, parentage-testing, or relationship-verification tool, and it makes no clinical or diagnostic claim about any individual.

### Advanced Search

A query builder allows filtering individuals by sex, disease affection status, death status, age range, genetic test results, clinical test results, treatments, and events. Searches support relational scope (parents, siblings, children, ancestors, descendants) with AND/OR match modes.

### Data Exchange

| Format | Import | Export | Notes |
|--------|--------|--------|-------|
| JSON | Yes | Yes | Full pedigree snapshot |
| GEDCOM 5.5.1 | Yes | Yes | Genealogy interoperability |
| GA4GH Phenopackets v2 | Yes | Yes | GA4GH genomics interoperability — phenotype (HPO) and pedigree exchange |
| XEG | Yes | — | Legacy Evagene v1 migration |
| 23andMe | Yes | — | Genotype, ancestry, traits, health history, conflict resolution |
| Image | Yes | — | OCR and shape detection from pedigree chart images |
| ChatGPT Custom GPT | Yes | — | Evagene Pedigree Builder — natural-language family description in, Evagene JSON file out |
| PNG | — | Yes | Configurable scale (1x–4x) |
| SVG | — | Yes | Vector output |
| PDF | — | Yes | A4/A3/Letter/Legal, portrait/landscape |
| CanRisk / BOADICEA v4 | — | Yes | Tab-separated `##CanRisk 2.0` header; upload at canrisk.org (BOADICEA not bundled — licensed by Univ. of Cambridge) |

**Evagene Pedigree Builder (ChatGPT Custom GPT).** A natural-language entry point alongside gesture drawing, keyboard shortcuts, GEDCOM import, 23andMe import, and OCR. The user describes a family in plain English inside ChatGPT; the GPT asks clarifying questions where the structure is ambiguous, then produces a downloadable Evagene-compatible pedigree JSON file. The file is loaded into Evagene via File → Load pedigree → Load Evagene file, at which point the pedigree renders with standard notation and is available for annotation, risk analysis, and export. This is a Route A integration: the GPT produces a file, a human loads it — no live API call from ChatGPT into Evagene. A Route B variant using OpenAI Actions against the Evagene API is planned but not yet built. OpenAI requires a paid ChatGPT subscription (Plus, Team, or Enterprise) to use any Custom GPT; this is not an Evagene paywall. The GPT is strictly a data-capture aid — it does not give medical advice, diagnose, or run risk models. Live URL: https://chatgpt.com/g/g-69ea28b554b8819191ae0f8fd2406d52-evagene-pedigree-builder. Landing page: https://evagene.com/pedigree-builder-gpt.

---

## Who Evagene Is For

Evagene is an educational and research tool. It is used for teaching, training, documentation, and exploratory research — not for clinical decision-making. Professional users are addressed as educators, researchers, and learners, not as operators of a clinical-workflow tool.

### Research Geneticists
Mendelian modelling with full parameter control. Linkage analysis with LOD scores, flanking markers, haplotype tables. Marker management. Species flexibility. Genotype-phenotype correlation. GEDCOM export. Full research and teaching surface for the implemented algorithm families.

### Clinical Geneticists (teaching, research, documentation)
Structured pedigree documentation with accurate standard notation for teaching trainees and running research projects. Implementations of published risk-model algorithms for educational exploration on anonymised / synthetic pedigrees. Comprehensive family-history data capture, batch investigation, linkage analysis. Not for clinical decision-making — for clinical workflow, use regulated clinical software and route BOADICEA via canrisk.org.

### Genetic Counsellors & Nurses (teaching, training, documentation)
Plain-language educational summaries. Consent tracking. Contact information management. Proband identification. Role-specific teaching workflow guides. Not for clinical decision-making.

### Oncologists (teaching and research)
Educational exploration of published BRCAPRO, MMRpro, and PancPRO algorithms on anonymised / synthetic pedigrees. Tumour characterisation for research documentation. Treatment and manifestation timeline capture. Not for clinical decision-making.

### General Practice Doctors (education and documentation)
Three-generation pedigree documentation for training and reference. Published risk-model algorithm implementations for education. Structured family-history documentation. Not intended for clinical decision-making or referral triage.

### Patients & Families (personal family-history documentation)
Easy gesture-based drawing. Visual clarity with colour-coded disease sectors. 23andMe data import. Image import from paper pedigrees. PNG/SVG/PDF export for sharing. Plain-language educational summaries — **not medical advice, not a substitute for consultation with a clinician.**

### Genealogists
GEDCOM 5.5.1 import/export for Ancestry, FamilySearch, Gramps compatibility. Rich family data capture. Multi-generation support. Twin documentation. Automatic consanguinity detection.

### Educators & Students
1,900+ help guides across six catalogues (diseases, traits, allergies, clinical tests, markers / genes, treatments) with cross-linking and authoritative external references (LOINC, NCBI Gene, OMIM, ClinVar, RxNorm, BNF, DrugBank). Introductory through advanced genetics guides. Interactive exploration. Standard notation enforcement. Risk model documentation with canonical citations (Carter 1961, Falconer 1965, Claus 1994, Couch 1997, Frank 2002, Evans 2004, Vasen 1999, Umar 2004, Gail 1989, Tyrer/Duffy/Cuzick 2004, Antoniou 2004 / Lee 2019). Browse the catalogue at https://evagene.net/help/#browse.

---

## Platform & Integrations

Evagene includes a platform layer that turns pedigree intelligence into infrastructure for external systems and AI agents.

### API Keys
Long-lived, scoped, rate-limited keys for programmatic access to the full REST API. Format: evg_<43 characters> (256-bit entropy). SHA-256 hashed at rest. Three scopes: read, write, analyse (write and analyse imply read). Configurable per-minute (default 60) and per-day (default 10,000) rate limits with sliding window enforcement. Maximum 20 keys per user. Optional expiry dates. Authentication via X-API-Key header or ?api_key= query parameter.

### Bring Your Own Key (BYOK) LLM
Users can supply their own Anthropic (Claude) or OpenAI (GPT) API key for all AI interpretation and template execution. Supported providers: Anthropic (default model claude-sonnet-4-20250514) and OpenAI (default model gpt-4o). Keys are encrypted at rest using Fernet (AES-128-CBC + HMAC-SHA256), keyed from the server's JWT secret. When configured, BYOK bypasses the standard rolling 24-hour quota. Users can override the default model to use any model their provider supports.

### Webhooks
Push HMAC-SHA256 signed HTTP POST notifications when pedigree data changes. Eight event types: pedigree.created, pedigree.updated, pedigree.deleted, individual.created, individual.updated, individual.deleted, analysis.completed, import.completed. Each webhook has a unique secret for signature verification. Payloads include X-Evagene-Event, X-Evagene-Signature-256, and X-Evagene-Delivery headers. Maximum 20 webhooks per user. Delivery history tracks the last 20 attempts per webhook.

### Analysis Templates
Reusable custom AI prompt templates with variable injection. Templates have a system prompt (AI role) and a user prompt template with placeholders: {{pedigree_description}}, {{proband_name}}, {{proband_sex}}, {{disease_list}}, {{risk_summary}}. Variables are replaced with computed values at execution time. Templates can be shared publicly. Maximum 50 per user. Execution uses BYOK key or server default (subject to quota).

### MCP Server (Model Context Protocol)
Stdio-mode MCP server exposing 27 tools to AI agents: pedigree tools (list_pedigrees, get_pedigree, create_pedigree, add_individual, update_individual, add_relationship, add_offspring, describe_pedigree, get_pedigree_summary, export_gedcom, import_gedcom), help-catalogue tools (list_guide_categories, search_guides, get_guide), related_concepts (educational correlation graph; always carries the educational-use disclaimer), and tools covering the newer educational / research surfaces — HPO phenotyping (browse / search the HPO catalogue and record observed or excluded phenotype features), phenotype-to-gene educational associations (candidate associated genes as reference data only — never a ranked likelihood or diagnosis), disease-ontology cross-references (ICD-10 / OMIM / MONDO / Orphanet / DOID), GA4GH Phenopackets v2 import and export, and the relatedness / IBD analysis (pairwise kinship, inbreeding, Jacquard k0 / k1 / k2; educational / research, never forensic). Authenticated via EVAGENE_API_KEY environment variable. Connects directly to SQLite database (no HTTP roundtrip). Compatible with Claude Desktop, Claude Code, and any MCP-capable client. Changes are immediately visible in the web UI.

### Embeddable Pedigree Viewer
Drop-in pedigree diagrams for third-party websites via three methods: (1) Full HTML page via iframe at /api/embed/{pedigree_id}, (2) Raw SVG at /api/embed/{pedigree_id}/svg, (3) JavaScript snippet at /api/embed/snippet.js that auto-discovers data-evagene-pedigree attributes. SVG uses standard pedigree notation: square=male, circle=female, diamond=unknown, solid fill=affected, centre dot=carrier, diagonal line=deceased, arrow=proband. Authentication via API key or public pedigree flag. Responsive SVG with viewBox scaling (max 1200x900).

Full platform documentation: https://evagene.net/help/platform_overview

## Research & Third-Party Record

- [Research & Citations](https://evagene.com/research-citations.html) — Peer-reviewed papers citing Evagene (Marfan syndrome case study, NPHP4 variant report, retinitis pigmentosa docking study, MDPI *Bioengineering* methods review recommending Evagene), with author institutions (Semmelweis University, Birjand/Kerman/Shahid Beheshti/Shahid Sadoughi Universities of Medical Sciences, University of Guilan, and others) and the U.S. Department of Veterans Affairs Technical Reference Model listing.

---

## Help & Documentation

Evagene includes 1,900+ help guides accessible at https://evagene.net/help. Six cross-linked catalogues — diseases, traits, allergies, clinical tests (LOINC-linked), markers / genes (NCBI Gene, OMIM, ClinVar), and treatments (RxNorm, BNF, DrugBank) — plus educational guides, role-specific workflows, and risk-model documentation:

### Educational Guides
- Introduction to Genetics — DNA, genes, chromosomes, inheritance patterns, pedigree charts, genetic testing, cancer genetics, consanguinity, twins, ancestry, pharmacogenomics, genomic data
- Intermediate Genetics — Mendelian inheritance in depth, linkage, population genetics, cytogenetics, epigenetics, multifactorial inheritance, prenatal genetics
- Advanced Genetics — Molecular genetics, genomics, statistical genetics
- Clinical Genetics for Patients — Plain-language guide to genetic services
- Clinical Genetics for Medical Professionals — Clinical genetics reference

### Role-Specific Workflow Guides
- Clinical Geneticist (basic + advanced)
- Oncologist (basic + advanced)
- General Practice Doctor (basic + advanced)
- Genetic Nurse / Counsellor (basic + advanced)
- Research Geneticist (basic + advanced)
- Genealogist (basic + advanced)
- Patient / Family Member (basic + advanced)

### Reference Documentation
- Features & Benefits — Complete feature overview
- Risk Models — BRCAPRO, MMRpro, PancPRO, Mendelian models, linkage analysis
- Disease Catalogue — 230+ diseases with ICD-10, OMIM, inheritance patterns
- Allergy Catalogue — 55+ allergies across 6 categories
- Trait Catalogue — 50+ traits across 6 categories
- Clinical Test Catalogue — Test types and reference ranges
- Intervention Catalogue — Treatment and medication categories
- Keyboard Shortcuts — Complete shortcut reference

### Disease-Specific Guides (230+ guides)
Individual guides for each disease in the catalogue, covering genetics, symptoms, testing, prognosis, and how to use Evagene for analysis. Diseases include:
Achondroplasia, Alagille Syndrome, Alzheimer's Disease (familial), Angelman Syndrome, Breast Cancer (hereditary), Brugada Syndrome, Charcot-Marie-Tooth Disease, Cystic Fibrosis, Down Syndrome, Duchenne Muscular Dystrophy, Ehlers-Danlos Syndrome, Fabry Disease, Familial Adenomatous Polyposis, Familial Hypercholesterolaemia, Fragile X Syndrome, Friedreich's Ataxia, Gaucher Disease, Haemophilia A/B, Hereditary Breast and Ovarian Cancer Syndrome, Huntington's Disease, Hypertrophic Cardiomyopathy, Li-Fraumeni Syndrome, Long QT Syndrome, Lynch Syndrome, Marfan Syndrome, Multiple Endocrine Neoplasia (Type 1 & 2), Myotonic Dystrophy, Neurofibromatosis (Type 1 & 2), Noonan Syndrome, Osteogenesis Imperfecta, Phenylketonuria, Polycystic Kidney Disease, Retinoblastoma, Sickle Cell Disease, Spinal Muscular Atrophy, Tay-Sachs Disease, Thalassaemia, Tuberous Sclerosis, Turner Syndrome, Von Hippel-Lindau Syndrome, Von Willebrand Disease, Williams Syndrome, Wilson's Disease, and 140+ more.

---

## Frequently Asked Questions

### What is Evagene?
Evagene is a web-based academic, research, and educational pedigree modelling platform for teaching, training, research, and family-history documentation. It lets users draw, annotate, and explore family pedigrees with standard genetic notation, implementations of published BayesMendel risk-model algorithms (BRCAPRO, MMRpro, PancPRO), Mendelian inheritance teaching models, AI-assisted draft summaries for educational review, blood type and trait inference from 23andMe SNP data, a 230+ disease catalogue, and interoperability with GEDCOM, 23andMe, and other formats. Not a medical device; not intended for clinical decision-making.

### What is BRCAPRO and how does Evagene use it?
BRCAPRO is a Bayesian statistical model that estimates the probability of carrying a BRCA1 or BRCA2 mutation and projects future breast and ovarian cancer risk based on family history. Evagene integrates BRCAPRO via the BayesMendel R package. Users draw a family pedigree, mark cancer diagnoses with ages, and run the model directly within the application.

### Can I import 23andMe data into Evagene?
Yes. Evagene supports importing 23andMe raw genotype data, ancestry composition, DNA relatives, traits, and health history. Imported SNP markers are used to automatically infer ABO blood type, Rh factor, and FUT2 secretor status. A conflict resolution dialog handles cases where imported data differs from existing records.

### Does Evagene support GEDCOM import and export?
Yes. Evagene supports GEDCOM 5.5.1, the universal genealogy interchange format. You can import pedigrees from Ancestry, FamilySearch, Gramps, and other genealogy software, and export pedigrees back to GEDCOM for sharing.

### Does Evagene support data governance and consent tracking?
Yes. Each individual in a pedigree has a consent-to-share flag that can be set in the properties panel, supporting clinical data governance requirements.

### Is Evagene free?
Evagene is currently in alpha and available free of charge via the waiting list at https://evagene.com.

### Does Evagene use AI to generate draft pedigree summaries?
Yes. Evagene integrates AI to generate draft educational summaries of pedigrees for researcher and learner review. The AI analyses family structure, documented findings, and inheritance-pattern observations, then produces a summary covering structural observations, documentation gaps, data-completeness prompts, and discussion prompts linked to published literature. These are drafts for human review — not clinical advice, not diagnostic output, and not intended to inform clinical decisions.

### Can Evagene infer blood type from genetic data?
Yes. After importing 23andMe genotype data, Evagene automatically infers ABO blood type, Rh factor, and FUT2 secretor status from SNP markers. Inferred traits are displayed as visual cards in the properties panel and can be overridden manually.

### What is risk screening in Evagene?
Risk screening lets you designate a proband and screen them against all diseases in your collection simultaneously. Evagene runs the appropriate risk model for each disease and produces carrier probabilities, colour-coded risk levels, family member risk tables, a risk karyogram showing elevated-risk gene loci, differential diagnosis for affected siblings from unaffected parents, and optional descendant reports.

### Who makes Evagene?
Evagene is developed independently as a specialist tool for clinical genetics and pedigree management.

---

## Topic Guides

Evagene publishes in-depth educational guides on its website:

### Pillar pages

- [Pedigree Drawing Software](https://evagene.com/pedigree-drawing-software.html) — How to draw a pedigree chart, standard notation, and comparison of pedigree drawing tools
- [Hereditary Cancer Risk Assessment](https://evagene.com/hereditary-cancer-risk-assessment.html) — Understanding BRCAPRO, MMRpro, PancPRO, and Bayesian cancer risk modelling from family pedigrees
- [GEDCOM & Genealogy](https://evagene.com/gedcom-pedigree-software.html) — GEDCOM 5.5.1 import/export, 23andMe data integration, and bridging genealogy with clinical genetics
- [Clinical Genetics Pedigree Tool](https://evagene.com/clinical-genetics-pedigree-tool.html) — What clinical geneticists and genetic counsellors need from pedigree software
- [Mendelian Inheritance Calculator](https://evagene.com/mendelian-inheritance-calculator.html) — Autosomal dominant, autosomal recessive, and X-linked recessive inheritance models with worked examples
- [Platform & Integrations](https://evagene.com/platform.html) — API keys, BYOK LLM, webhooks, analysis templates, MCP server, and embeddable pedigree viewer

### Hubs

- [Everything Evagene Does — Complete Feature List](https://evagene.com/features.html) — the single-page catalogue of every capability on this site (drawing, intake, catalogues, the twenty-one risk models, phenotyping, interoperability, the platform and 27-tool MCP layer, and the 25 open-source MIT integration examples at github.com/xiasma/evagene-integration-examples)
- [Compare Evagene](https://evagene.com/compare.html) — side-by-side comparisons vs every major clinical pedigree platform
- [Alternatives field guides](https://evagene.com/alternatives.html) — "alternatives-to-X" guides for eight major products

### Evagene-vs competitor comparisons

Evagene is compared honestly against every major clinical pedigree tool. Claims are drawn from each competitor's public website as of April 2026. The UK Trade Marks Act 1994 s.10(6) and Business Protection from Misleading Marketing Regulations 2008 protect honest comparative advertising.

- [Phenotips vs Evagene](https://evagene.com/phenotips-vs-evagene.html)
- [Progeny vs Evagene](https://evagene.com/progeny-vs-evagene.html)
- [Progeny Cloud vs Evagene](https://evagene.com/progeny-cloud-vs-evagene.html)
- [TrakGene vs Evagene](https://evagene.com/trakgene-vs-evagene.html)
- [FamGenix vs Evagene](https://evagene.com/famgenix-vs-evagene.html)
- [CanRisk vs Evagene](https://evagene.com/canrisk-vs-evagene.html)
- [QuickPed vs Evagene](https://evagene.com/quickped-vs-evagene.html)
- [PedigreeTool vs Evagene](https://evagene.com/pedigreetool-vs-evagene.html)
- [GenoPro vs Evagene](https://evagene.com/genopro-vs-evagene.html)
- [f-tree vs Evagene](https://evagene.com/f-tree-vs-evagene.html)
- [ConceptViz vs Evagene](https://evagene.com/conceptviz-vs-evagene.html)
- [genoDraw vs Evagene](https://evagene.com/genodraw-vs-evagene.html)
- [PERSEUS vs Evagene](https://evagene.com/perseus-vs-evagene.html)
- [SmartDraw vs Evagene](https://evagene.com/smartdraw-pedigree-vs-evagene.html)
- [Creately vs Evagene](https://evagene.com/creately-pedigree-vs-evagene.html)
- [Visual Paradigm vs Evagene](https://evagene.com/visual-paradigm-pedigree-vs-evagene.html)
- [Edraw vs Evagene](https://evagene.com/edraw-pedigree-vs-evagene.html)
- [CloudAiry vs Evagene](https://evagene.com/cloudairy-vs-evagene.html)

### Cross-competitor comparisons (Evagene as neutral referee)

- [Phenotips vs Progeny](https://evagene.com/phenotips-vs-progeny.html)
- [TrakGene vs Phenotips](https://evagene.com/trakgene-vs-phenotips.html)
- [FamGenix vs Phenotips](https://evagene.com/famgenix-vs-phenotips.html)
- [FamGenix vs Progeny](https://evagene.com/famgenix-vs-progeny.html)
- [BOADICEA vs BRCAPRO](https://evagene.com/boadicea-vs-brcapro.html)

### Migration guides

- [Migrating from Genial PedigreeDraw](https://evagene.com/migrating-from-genial-pedigree-draw.html) — Genial was discontinued in May 2020

### Alternatives field guides

- [Alternatives to Phenotips](https://evagene.com/alternatives-to-phenotips.html)
- [Alternatives to Progeny](https://evagene.com/alternatives-to-progeny.html)
- [Alternatives to TrakGene](https://evagene.com/alternatives-to-trakgene.html)
- [Alternatives to FamGenix](https://evagene.com/alternatives-to-famgenix.html)
- [Alternatives to CanRisk](https://evagene.com/alternatives-to-canrisk.html)
- [Alternatives to GenoPro](https://evagene.com/alternatives-to-genopro.html)
- [Alternatives to PedigreeTool](https://evagene.com/alternatives-to-pedigreetool.html)
- [Alternatives to QuickPed](https://evagene.com/alternatives-to-quickped.html)

### Best-of roundups

- [Best pedigree software 2026](https://evagene.com/best-pedigree-software-2026.html)
- [Best free pedigree makers](https://evagene.com/best-free-pedigree-makers.html)
- [Best pedigree software for genetic counsellors](https://evagene.com/best-pedigree-software-for-genetic-counsellors.html)
- [Best pedigree software for hospitals](https://evagene.com/best-pedigree-software-for-hospitals.html)
- [Best pedigree software for oncology](https://evagene.com/best-pedigree-software-for-oncology.html)
- [Best pedigree software for research](https://evagene.com/best-pedigree-software-for-research.html)
- [Best clinical genetics software](https://evagene.com/best-clinical-genetics-software.html)
- [Best hereditary cancer risk tools](https://evagene.com/best-hereditary-cancer-risk-tools.html)

### Cancer risk model calculator hubs

- [BRCAPRO calculator](https://evagene.com/brcapro-calculator.html) — BRCA1/BRCA2 carrier probability and breast/ovarian cancer risk
- [MMRpro calculator](https://evagene.com/mmrpro-calculator.html) — Lynch syndrome mismatch repair gene carrier probability
- [PancPRO calculator](https://evagene.com/pancpro-calculator.html) — familial pancreatic cancer susceptibility
- [Lynch syndrome risk calculator](https://evagene.com/lynch-syndrome-risk-calculator.html)
- [Tyrer-Cuzick alternative](https://evagene.com/tyrer-cuzick-alternative.html) — Tyrer-Cuzick / IBIS model context
- [BOADICEA alternative](https://evagene.com/boadicea-alternative.html) — BOADICEA / CanRisk model context
- [Breast cancer family history calculator](https://evagene.com/breast-cancer-family-history-calculator.html)
- [Ovarian cancer family history calculator](https://evagene.com/ovarian-cancer-family-history-calculator.html)
- [Pancreatic cancer family history](https://evagene.com/pancreatic-cancer-family-history.html)

### Mendelian / inheritance calculator hubs

- [Autosomal dominant calculator](https://evagene.com/autosomal-dominant-calculator.html)
- [Autosomal recessive calculator](https://evagene.com/autosomal-recessive-calculator.html)
- [X-linked recessive calculator](https://evagene.com/x-linked-recessive-calculator.html)
- [Carrier probability calculator](https://evagene.com/carrier-probability-calculator.html)
- [Inheritance pattern identifier](https://evagene.com/inheritance-pattern-identifier.html)
- [Consanguinity calculator / Wright's coefficient](https://evagene.com/consanguinity-calculator.html)

### Germline mosaicism and condition-specific pedigree guides

Evagene computes parental germline mosaicism posterior probability from pedigree structure, with optional somatic variant allele fraction (VAF) input from blood or sperm sequencing and joint-parent logic that properly exonerates one parent when the other is confirmed mosaic. The disease catalogue stores per-condition `de_novo_rate`, `germline_mosaicism_rate`, and `germline_mosaicism_sex_bias` (paternal / maternal), which parameterise the posterior correctly for each disorder. None of the major clinical pedigree platforms advertises this calculation publicly as of April 2026.

- [Germline mosaicism calculator](https://evagene.com/germline-mosaicism-calculator.html) — the core methodology page with worked scenarios (DMD, achondroplasia, osteogenesis imperfecta, tuberous sclerosis, Dravet, Rett)
- [Duchenne muscular dystrophy pedigree](https://evagene.com/duchenne-muscular-dystrophy-pedigree.html) — X-linked recessive, maternal blood VAF paradigm
- [Dravet syndrome pedigree](https://evagene.com/dravet-syndrome-pedigree.html) — SCN1A, autosomal dominant, 90% de novo, 7% germline mosaicism
- [Rett syndrome pedigree](https://evagene.com/rett-syndrome-pedigree.html) — MECP2, X-linked dominant with paternal de novo bias, female-specific
- [Osteogenesis imperfecta pedigree](https://evagene.com/osteogenesis-imperfecta-pedigree.html) — the classic two-lethal-neonates counselling case
- [Achondroplasia pedigree](https://evagene.com/achondroplasia-pedigree.html) — FGFR3 c.1138G>A, paternal-age effect, measurable sperm VAF
- [Tuberous sclerosis pedigree](https://evagene.com/tuberous-sclerosis-pedigree.html) — three-affected-children scenario with mosaic vs reduced-penetrance posterior split

### Pedigree notation, tutorial, and pillar guides

The pedigree pillar pages are the canonical entry points for the four highest-volume search queries in this space:

- [Pedigree drawing tool](https://evagene.com/pedigree-drawing-tool.html) — pillar for "pedigree drawing tool"; in-browser pedigree drawing tool with NSGC notation, gesture drawing, GEDCOM and CanRisk export, and twenty-one published risk-model algorithm implementations
- [Pedigree chart](https://evagene.com/pedigree-chart.html) — pillar for "pedigree chart"; definition, symbols, three-generation capture, inheritance patterns visible in a pedigree
- [Clinical pedigree drawing](https://evagene.com/clinical-pedigree-drawing.html) — pillar for "clinical pedigree drawing"; NSGC 2022 conventions, three-generation capture, consanguinity loops, pregnancy outcomes, and the boundary between in-tool and canonical computation
- [Pedigree drawing software](https://evagene.com/pedigree-drawing-software.html) — pillar for "pedigree drawing"; complete guide with software comparison
- [Pedigree chart maker](https://evagene.com/pedigree-chart-maker.html) — supporting page for the "pedigree chart maker" variant query
- [Pedigree drawing online](https://evagene.com/pedigree-drawing-online.html) — supporting page for the "pedigree drawing online" variant query
- [Clinical pedigree drawing guidelines](https://evagene.com/clinical-pedigree-drawing-guidelines.html) — NSGC 1995, 2008, 2022 standards, plus ISCN, HGNC, HPO context
- [NSGC pedigree notation](https://evagene.com/nsgc-pedigree-notation.html) — NSGC 1995 / 2008 / 2022 standards
- [ISCN pedigree symbols](https://evagene.com/iscn-pedigree-symbols.html)
- [Standard pedigree nomenclature](https://evagene.com/standard-pedigree-nomenclature.html)
- [How to draw a pedigree chart](https://evagene.com/how-to-draw-a-pedigree-chart.html)
- [Pedigree chart in 5 simple steps](https://evagene.com/pedigree-chart-5-steps.html)
- [Pedigree symbols reference](https://evagene.com/pedigree-symbols-reference.html)
- [Pedigree chart examples by inheritance pattern](https://evagene.com/pedigree-chart-examples.html)
- [Three-generation family history](https://evagene.com/three-generation-family-history.html)
- [Free online pedigree maker guide](https://evagene.com/free-online-pedigree-maker.html)
- [Pedigree chart template](https://evagene.com/pedigree-chart-template.html)
- [Gender-inclusive pedigree drawing](https://evagene.com/gender-inclusive-pedigree-drawing.html)
- [Pedigree chart for biology class](https://evagene.com/pedigree-chart-biology-class.html)

### Platform, API and integration guides

- [Pedigree REST API](https://evagene.com/pedigree-api.html) — scoped keys, rate limits, endpoints
- [Pedigree MCP server](https://evagene.com/pedigree-mcp-server.html) — 27 tools for Claude Desktop, Claude Code, and any MCP-compatible AI agent
- [LLM pedigree analysis](https://evagene.com/llm-pedigree-analysis.html) — BYOK with Anthropic Claude and OpenAI GPT
- [Embeddable pedigree viewer](https://evagene.com/embeddable-pedigree-viewer.html) — iframe, raw SVG, or JavaScript snippet
- [HL7 FHIR pedigree](https://evagene.com/hl7-fhir-pedigree.html) — FHIR FamilyMemberHistory and Genomics IG
- [EHR pedigree integration](https://evagene.com/ehr-pedigree-integration.html) — Epic, Oracle Health / Cerner integration patterns
- [GEDCOM to pedigree converter](https://evagene.com/gedcom-to-pedigree-converter.html)
- [Phenopackets pedigree](https://evagene.com/phenopackets-pedigree.html) — GA4GH Phenopackets v2 interoperability

### Related Concepts (educational correlation graph)

- [Related Concepts Explorer](https://evagene.com/related-concepts-explorer.html) — the full correlation graph: two edge sources (curated + marker-derived), eight relationship types, status-qualified clinical-test edges, the Related concepts editor panel, and /api/correlations + MCP related_concepts access. Educational reference data, not risk analysis or diagnosis
- [Biomarker & condition associations](https://evagene.com/biomarker-disease-associations.html) — status-qualified clinical-test edges (low vs high), worked through the iron studies (ferritin, transferrin saturation, MCV)
- [Gene & shared-gene associations](https://evagene.com/gene-disease-associations.html) — the auto-derived genetic_association and shared_gene edges from the marker catalogue (BRCA2, PTEN, GBA, MITF examples); educational genotype–phenotype exploration, not risk prediction
- [Genetics concept map](https://evagene.com/genetics-concept-map.html) — using the Related Concepts explorer as a teaching concept map (pleiotropy, lab panels, associated conditions)

### Genealogy and consumer crossover

- [Genogram maker online](https://evagene.com/genogram-maker-online.html)
- [Medical family tree](https://evagene.com/medical-family-tree.html)
- [23andMe pedigree import](https://evagene.com/23andme-pedigree-import.html)
- [Family health history online](https://evagene.com/family-health-history-online.html)
- [Genogram vs pedigree](https://evagene.com/genogram-vs-pedigree.html)
- [Medical genogram software](https://evagene.com/medical-genogram-software.html)
- [AI genogram maker](https://evagene.com/ai-genogram-maker.html)

### Specialised clinical guides

- [Rare disease pedigree software](https://evagene.com/rare-disease-pedigree-software.html)
- [Hereditary cardiac pedigree](https://evagene.com/hereditary-cardiac-pedigree.html)
- [Karyogram viewer](https://evagene.com/karyogram-viewer.html)
- [Pedigree OCR](https://evagene.com/pedigree-ocr.html)
- [Batch pedigree risk screening](https://evagene.com/batch-pedigree-risk-screening.html)

### Persona guides

- [For clinical geneticists](https://evagene.com/for-clinical-geneticists.html)
- [For genetic counsellors](https://evagene.com/for-genetic-counsellors.html)
- [For oncologists](https://evagene.com/for-oncologists.html)
- [For general practitioners](https://evagene.com/for-general-practitioners.html)
- [For research geneticists](https://evagene.com/for-research-geneticists.html)
- [For genetic nurses](https://evagene.com/for-genetic-nurses.html)
- [For genealogists](https://evagene.com/for-genealogists.html)
- [For educators and students](https://evagene.com/for-educators-students.html)
- [For patients and families](https://evagene.com/for-patients-families.html)

### UK and NHS guides

- [Pedigree software for the NHS](https://evagene.com/pedigree-software-nhs.html)
- [Pedigree software for UK clinicians](https://evagene.com/pedigree-software-uk-clinicians.html)

---

## Learning Hub

- [Learn Genetics — reading pathways](https://evagene.com/learn-genetics.html) — Microsoft-Learn-style pathway hub that organises the educational library into seven structured reading pathways. Each pathway has a defined audience, prerequisite, time estimate, and ordered reading list with one-line page descriptions; an Apply What You've Learned section routes to twenty risk-model calculator pages and the in-browser pedigree drawing tool. Pathways: (1) Foundations &mdash; genetics from scratch; (2) Molecular biology deep dive; (3) Clinical genetics; (4) Cancer genetics; (5) Population & quantitative; (6) Therapeutics & gene therapy; (7) Refresher: recent advances. Free in the browser, no registration, no paywall. The page also includes a topic browser that lists every page organised under the 12 major topics for self-directed reading.

## Free Embeds

- [Embed pedigree drawing — free iframe](https://evagene.com/embed-pedigree-drawing.html) — drop-in iframe (`https://evagene.net/draw`) that puts the full Evagene pedigree drawing canvas inside any website, blog, course page, LMS module, or app. Visitors get gesture drawing, NSGC-compliant notation, disease annotation against the 1,900-entry catalogue, consanguinity detection with Wright's coefficient, and exports to PDF, PNG, SVG, GEDCOM 5.5.1, CanRisk 2.0, and Phenopackets v2. No install, no signup, no API key. The landing page includes a live demo (the iframe embedded on the page itself), a copy-ready snippet, customisation guidance (width / height / max-width / loading=lazy / referrerpolicy / accessibility title), use-case patterns (genetics teaching pages, biology textbook websites and OERs, university course pages and LMS modules, research-lab outreach pages, blog posts and articles, genealogy and personal family-history sites), a comparison table against the read-only Embeddable Pedigree Viewer, a privacy and alpha-boundary section, and an eight-question FAQ. Free during alpha for educational, research, and family-history-documentation use; not for clinical work or real patient data.
- [Embeddable pedigree viewer](https://evagene.com/embeddable-pedigree-viewer.html) — the complementary read-only display embed for a specific pedigree fetched from an Evagene account. Three embed modes (iframe, raw SVG, JavaScript snippet); API-key authentication for private pedigrees, public-pedigree mode for research figures and demos. Suits research dashboards and public-pedigree research figures rather than teaching / outreach contexts where the drawing embed is the right fit.

## Genetic Current — Daily Genetics News

- [Genetic Current](https://evagene.com/news/) — the daily-updated news section of evagene.com, summarising public-source genetics and genomics reporting for researchers, clinicians, educators, students, genealogists, and patients. The pipeline pulls RSS / Atom feeds from approximately sixteen trusted public sources (NHGRI, CDC Public Health Genomics, NHS England, Genomics England, the PHG Foundation, the Wellcome Sanger Institute, Cancer Research UK, The Conversation, PLOS Genetics, the Nature Medical Genetics subject feed, EurekAlert!, ScienceDaily, Stat News, The Scientist, and bioRxiv preprints), deduplicates against a 14-day window, and sends a daily batch to Claude (Sonnet 4.6) under a documented editorial brief. Claude clusters multiple write-ups of the same finding into one canonical story, scores each cluster on importance, audience breadth, and novelty, tags it with the relevant audience subset, and produces a 150–300 word factual summary plus (when patient-relevant) a separate plain-language patient version that ends with an explicit "educational summary, not medical advice" disclaimer. Stories are framed throughout as educational and research-oriented — never as medical advice, never as screening recommendations, never as clinical decision support. Source images are downloaded and rehosted only where the licence permits (public-domain US-gov sources, UK OGL, press-release editorial permission, CC BY); for all-rights-reserved or CC-BY-ND-text sources the renderer substitutes a category-illustration placeholder, avoiding both legal exposure and the privacy leakage of cross-origin hotlinks.

- Trending is computed by **cross-source consensus** rather than engagement metrics: stories covered by multiple distinct publishers within a recency window score higher than single-source items, with novelty and importance modifiers. REviewed daily at 07:00 UTC by GitHub Actions, with the rendered HTML committed back to the repository.

- Audience indices: [Researchers](https://evagene.com/news/researchers/) · [GPs](https://evagene.com/news/gps/) · [Oncologists](https://evagene.com/news/oncologists/) · [Genetic Counsellors](https://evagene.com/news/genetic-counsellors/) · [Educators](https://evagene.com/news/educators/) · [Students](https://evagene.com/news/students/) · [Genealogists](https://evagene.com/news/genealogists/) · [Patients & Families](https://evagene.com/news/patients/). Each story has a canonical permalink at `/news/YYYY/MM/DD/<slug>/` and is cross-linked from the audience indices it has been tagged with. The [Archive](https://evagene.com/news/archive/) lists every story by month. Full-text search (Pagefind, lazy-loaded, no third-party calls, no cookies) covers the news section and the wider Evagene site. Each story page carries native one-click share controls for X, LinkedIn, Facebook, Reddit, WhatsApp, Telegram, email, and copy-link.

## Educational Topic Library

A 46-page educational library covering the molecular, clinical, quantitative, population, and ethical genetics topics taught at MSc / FRCPath / equivalent level. Each page is a 1,300–2,000-word survey with inline citations to peer-reviewed papers, NCBI / OMIM / GeneReviews / ClinVar / gnomAD entries, and the standards-body resources (NSGC, ACMG/AMP, ISCN, HGNC, HPO, GA4GH).

The library is structured as 12 major topics, each with a pillar page and 2-3 subtopic pages. Citations span Mendel 1866 → Watson & Crick 1953 → Pauling 1949 → Jacob & Monod 1961 → Knudson 1971 → Bennett 1995/2008/2022 → ENCODE 2012 → gnomAD 2020 → AlphaMissense 2023 → Casgevy 2023.

Positioning is consistent with the rest of the site: research, education, and family-history documentation; not clinical decision support, not a medical device.

### Molecular Architecture of Genes

- [Molecular Architecture of Genes](https://evagene.com/molecular-architecture-of-genes.html) — pillar
- [DNA and Chromatin Organization](https://evagene.com/dna-and-chromatin-organization.html) — nucleotide chemistry, base pairing thermodynamics (SantaLucia 1998), DNA supercoiling, nucleosomes (Luger 1997), Hi-C (Lieberman-Aiden 2009), TADs (Dixon 2012; Nora 2012)
- [DNA Replication and Repair](https://evagene.com/dna-replication-and-repair.html) — origin licensing, polymerases (Kunkel & Bebenek 2000), Okazaki fragments, MMR (Modrich 2006) → Lynch syndrome, NER → xeroderma pigmentosum, BER, HR (BRCA1/BRCA2/RAD51), NHEJ
- [Genome Structure and Variation](https://evagene.com/genome-structure-and-variation.html) — repetitive DNA, transposons (Cordaux & Batzer 2009), CNV (Sebat 2004; Conrad 2010; Sudmant 2015), structural variant detection (Collins 2020 gnomAD-SV; Chaisson 2019 long-read)

### Gene Expression Mechanisms

- [Gene Expression Mechanisms](https://evagene.com/gene-expression-mechanisms.html) — pillar; central dogma (Crick 1970), splicing discovery (Berget/Moore/Sharp 1977; Chow 1977)
- [Transcriptional Machinery](https://evagene.com/transcriptional-machinery.html) — Pol I/II/III, Pol II structure (Cramer 2001), CTD cycle (Buratowski 2009), promoters (Smale & Kadonaga 2003), Mediator (Allen & Taatjes 2015), enhancer-promoter contact (Schoenfelder & Fraser 2019)
- [RNA Processing and Stability](https://evagene.com/rna-processing-and-stability.html) — spliceosome (Will & Lührmann 2011), alternative splicing (Wang 2008; Pan 2008), polyadenylation (Tian & Manley 2017), NMD (Lykke-Andersen & Jensen 2015)
- [Translation and Post-Translational Control](https://evagene.com/translation-and-post-translational-control.html) — ribosome structure (Ban 2000; Wimberly 2000), eIFs (Jackson 2010; Sonenberg & Hinnebusch 2009), ribosome profiling (Ingolia 2009), chaperones (Hartl 2011), PTMs

### Regulation of Gene Activity

- [Regulation of Gene Activity](https://evagene.com/regulation-of-gene-activity.html) — pillar; Lac operon (Jacob & Monod 1961); ENCODE 2012; Roadmap Epigenomics (Kundaje 2015)
- [Cis and Trans Regulatory Elements](https://evagene.com/cis-and-trans-regulatory-elements.html) — first enhancer (Banerji 1981), CTCF (Phillips & Corces 2009), super-enhancers (Whyte 2013; Hnisz 2013), JASPAR, ATAC-seq (Buenrostro 2013), GTEx eQTLs
- [Epigenetics and Chromatin Dynamics](https://evagene.com/epigenetics-and-chromatin-dynamics.html) — DNA methylation (Bird 2002), TET (Tahiliani 2009), Polycomb (Margueron & Reinberg 2011), X-inactivation (Lyon 1961), TADs, loop extrusion (Sanborn 2015; Fudenberg 2016)
- [Gene Regulatory Networks](https://evagene.com/gene-regulatory-networks.html) — network motifs (Milo 2002), feed-forward loops (Mangan & Alon 2003), miRNAs (Bartel 2018), lncRNAs (Quinn & Chang 2016), Perturb-seq (Dixit 2016; Replogle 2022)

### Mutation Biology and Consequences

- [Mutation Biology and Consequences](https://evagene.com/mutation-biology-and-consequences.html) — pillar; Auerbach & Robson 1947; Drake 1991
- [Types of Mutation](https://evagene.com/types-of-mutation.html) — point mutations, indels, repeat expansions (Mirkin 2007; La Spada & Taylor 2010), de novo SNV rate (Kong 2012), mutational signatures (Alexandrov 2013), paternal-age effect
- [Functional Consequences of Mutation](https://evagene.com/functional-consequences-of-mutation.html) — LoF (MacArthur 2014), gain-of-function, dominant negative (Veitia 2002), splice mutations (Jaganathan 2019 SpliceAI), TERT promoter (Horn 2013; Huang 2013), gnomAD allele-frequency filtering (Karczewski 2020)
- [Mutation Detection and Interpretation](https://evagene.com/mutation-detection-and-interpretation.html) — Illumina (Bentley 2008), DeepVariant (Poplin 2018), Ensembl VEP (McLaren 2016), ACMG/AMP (Richards 2015), ClinVar (Landrum 2018), AlphaMissense (Cheng 2023), CADD (Rentzsch 2019), REVEL (Ioannidis 2016)

### Chromosomes and Cell Division

- [Chromosomes and Cell Division](https://evagene.com/chromosomes-and-cell-division.html) — pillar; Tjio & Levan 1956; Lejeune 1959; Nowell & Hungerford 1960; Caspersson 1970
- [Chromosome Structure and Mapping](https://evagene.com/chromosome-structure-and-mapping.html) — telomerase (Greider & Blackburn 1985), shelterin (de Lange 2005), centromeres (Cleveland 2003), T2T-CHM13 (Nurk 2022)
- [Cell Cycle, Mitosis, Meiosis](https://evagene.com/cell-cycle-mitosis-meiosis.html) — cyclin-CDK (Hartwell, Hunt, Nurse Nobel work), G1 control (Sherr & Roberts 1999), spindle assembly checkpoint (Musacchio & Salmon 2007), SPO11 (Keeney 1997), PRDM9 (Baudat 2010)
- [Chromosomal Abnormalities](https://evagene.com/chromosomal-abnormalities.html) — meiotic non-disjunction (Hassold & Hunt 2001), Down/Edwards/Patau/Turner/Klinefelter, BCR-ABL1, microdeletion / microduplication syndromes, NIPT (Bianchi 2014)

### Mendelian Genetics and Gene Discovery

- [Mendelian Genetics and Gene Discovery](https://evagene.com/mendelian-genetics-and-gene-discovery.html) — pillar; Mendel 1866, Garrod 1902, Morgan 1910, Botstein 1980
- [Inheritance Patterns](https://evagene.com/inheritance-patterns.html) — autosomal dominant / recessive, X-linked, mitochondrial, imprinting (Reik & Walter 2001), Knudson two-hit
- [Pedigree Analysis and Variable Expression](https://evagene.com/pedigree-analysis-and-variable-expression.html) — NSGC nomenclature (Bennett 1995, 2008, 2022), penetrance, expressivity, mosaicism, Bayesian carrier-probability calculation
- [Mapping and Gene Identification](https://evagene.com/mapping-and-gene-identification.html) — LOD scores (Morton 1955), CFTR positional cloning (Riordan 1989; Kerem 1989), Risch & Merikangas 1996, GWAS (WTCCC 2007), exome sequencing (Ng 2009; Ng 2010), Matchmaker Exchange (Philippakis 2015)

### Quantitative and Complex Traits

- [Quantitative and Complex Traits](https://evagene.com/quantitative-and-complex-traits.html) — pillar; Fisher 1918; Falconer 1965; Carter 1961; Lynch & Walsh 1998
- [Polygenic Models](https://evagene.com/polygenic-models.html) — additive / dominance / epistatic effects, narrow- vs broad-sense heritability, PRS (LDpred — Vilhjálmsson 2015; PRS-CS — Ge 2019; PGS Catalog — Lambert 2021), polygenic CAD (Khera 2018), portability (Martin 2019)
- [Heritability and Liability](https://evagene.com/heritability-and-liability.html) — twin h² (Falconer's formula), GREML (Yang 2010, 2011), LDSC (Bulik-Sullivan 2015), missing heritability (Manolio 2009; Visscher 2008), Falconer threshold model, Carter 1961 multifactorial threshold
- [Gene-Environment Interaction](https://evagene.com/gene-environment-interaction.html) — GxE designs (Hunter 2005), Mendelian randomisation (Davey Smith & Hemani 2014), epigenetic mediation (Heijmans 2008 Dutch Hunger Winter)

### Population and Evolutionary Genetics

- [Population and Evolutionary Genetics](https://evagene.com/population-and-evolutionary-genetics.html) — pillar; Hardy 1908, Wright 1931, Fisher 1930, Kimura 1968 (neutral theory)
- [Allele Frequency Dynamics](https://evagene.com/allele-frequency-dynamics.html) — Hardy-Weinberg, mutation-selection balance, sickle/malaria balancing selection (Allison 1954), lactase persistence (Tishkoff 2007), positive selection (Sabeti 2007), the coalescent (Kingman 1982)
- [Demography and Population Structure](https://evagene.com/demography-and-population-structure.html) — F-statistics, PCA (Patterson, Price & Reich 2006), ADMIXTURE (Alexander 2009), Ashkenazi BRCA founders (Roa 1996), demographic inference (Schiffels & Durbin 2014), 1000 Genomes (Auton 2015)
- [Population Genetics Applications](https://evagene.com/population-genetics-applications.html) — pan-ethnic carrier screening (ACOG 2017), Wilson-Jungner 1968 criteria, expanded carrier screening (Bell 2011), 100,000 Genomes (Caulfield 2017), ELSI

### Haemoglobin and Development

- [Haemoglobin and Development Genetics](https://evagene.com/haemoglobin-and-development-genetics.html) — pillar; Pauling 1949 sickle as the first molecular disease; Ingram 1957; Nüsslein-Volhard & Wieschaus 1980 (1995 Nobel)
- [Haemoglobin Biology and Disorders](https://evagene.com/haemoglobin-biology-and-disorders.html) — α2β2 / γ / δ chains, the haemoglobin switch, sickle cell HBB c.20A>T β6 Glu→Val, balancing selection (Allison 1954), α- and β-thalassaemia genetics, Casgevy / exa-cel CRISPR therapy (Frangoul 2021)
- [Genes in Development](https://evagene.com/genes-in-development.html) — WNT, SHH, Notch, BMP/TGF-β, FGF, Hippo signalling; holoprosencephaly (Roessler 1996); FGFR3 dysplasia series (achondroplasia, hypochondroplasia, thanatophoric); RASopathies (Roberts & Tartaglia 2010); Marfan / Loeys-Dietz; CADASIL (Joutel 1996); Hedgehog medulloblastoma

### Cancer Genetics and Somatic Variation

- [Cancer Genetics and Somatic Variation](https://evagene.com/cancer-genetics-and-somatic-variation.html) — pillar; Knudson 1971; Hanahan & Weinberg 2000, 2011, 2022; Vogelstein 2013; PCAWG 2020
- [Oncogenes and Tumour Suppressors](https://evagene.com/oncogenes-and-tumour-suppressors.html) — RAS / MYC / BCR-ABL1 / HER2 / EGFR / BRAF activation routes; RB1, TP53, APC, BRCA1/2 tumour suppressors; gatekeeper / caretaker / landscaper (Kinzler & Vogelstein 1997); driver vs passenger
- [Inherited Cancer Predisposition](https://evagene.com/inherited-cancer-predisposition.html) — HBOC (Antoniou 2003; Kuchenbaecker 2017); Lynch (Vasen 1999; Umar 2004; Møller 2018 PLSD); FAP / MAP; Li-Fraumeni (Frebourg 2020); Cowden; Peutz-Jeghers (Beggs 2010); juvenile polyposis (Blair 2020); HDGC; VHL; MEN1/2; NF1/2; TSC; retinoblastoma
- [Somatic Genomics](https://evagene.com/somatic-genomics.html) — clonal evolution (Nowell 1976); ctDNA (Wan 2017); CHIP (Genovese 2014); mutational signatures (Alexandrov 2013, 2020); HRD (Davies 2017); MSI; TMB; targeted-therapy biomarkers; MSI-H + checkpoint inhibitors (Le 2015); TRACERx (Jamal-Hanjani 2017)

### Metabolic Genetics and Therapeutics

- [Metabolic Genetics and Therapeutics](https://evagene.com/metabolic-genetics-and-therapeutics.html) — pillar; Garrod 1902, Beadle & Tatum 1941, Vogel 1959
- [Inborn Errors of Metabolism](https://evagene.com/inborn-errors-of-metabolism.html) — IEM categories (amino-acid, urea-cycle, organic-acidaemia, fatty-acid-oxidation, lysosomal storage, peroxisomal, mitochondrial, GSD, CDG); newborn screening (Guthrie 1963; Levy 2010); diagnostic exome (Yang 2013)
- [Pharmacogenetics and Precision Therapy](https://evagene.com/pharmacogenetics-and-precision-therapy.html) — CYP2D6 / 2C19 / 2C9 / 3A4 / 3A5; HLA-B*57:01 / abacavir (Mallal 2008); CPIC (Caudle 2014); Luxturna (Russell 2017); Zolgensma (Mendell 2017); Spinraza (Finkel 2017); CRISPR-Cas9 (Jinek 2012; Doudna & Charpentier 2014); base editing (Komor 2016); prime editing (Anzalone 2019); exa-cel / Casgevy (Frangoul 2021)

### Clinical Practice, Ethics, and Communication

- [Clinical Practice, Ethics, and Communication](https://evagene.com/clinical-practice-ethics-communication.html) — pillar; Reed 1947, Resta 2006 definition of genetic counseling, NSGC founded 1979
- [Clinical Genetic Skills](https://evagene.com/clinical-genetic-skills.html) — structured family-history interview, three-generation pedigree, NSGC 2022 (Bennett 2022), red-flag features per NICE CG164 / NG101, dysmorphology, case vignettes
- [Diagnostics and Counselling](https://evagene.com/diagnostics-and-counselling.html) — test taxonomy, ACMG/AMP (Richards 2015), secondary findings (Kalia 2017; Miller 2023 SF v3.2), Reciprocal-Engagement Model (Veach 2007), cascade testing (Sturm 2018), duty to warn (ASHG 1998)
- [Ethics, Legal and Social Issues](https://evagene.com/ethics-legal-social-issues.html) — NHGRI ELSI 1990; GINA 2008; GDPR Article 9; ABC v St George's [2020] EWHC 455 (QB); familial DNA searching (Bieber 2006); FDA / 23andMe 2013; Sirugo 2019 missing diversity; H3Africa; All of Us; Our Future Health; Newborn Genomes Programme; polygenic embryo selection (Karavani 2019; Turley 2021)

---

*For the latest information, visit https://evagene.com or https://evagene.net/help. For a complete list of indexable pages, see the [XML sitemap](https://evagene.com/sitemap.xml).*