# Evagene

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

Evagene is a browser-based platform for drawing, managing, and modelling family pedigrees. It combines a canvas editor with structured family-history data, implementations of twenty-one published risk-model algorithms across four families (Mendelian, polygenic / multifactorial liability-threshold, cancer family-history scoring, and a CanRisk / BOADICEA export bridge), and interoperability with genealogy and genomics 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.

## Key Facts

- Website: https://evagene.com
- Application: https://evagene.net
- Status: Alpha (free access via waiting list)
- Type: Web application (browser-based, no installation required)
- Category: Pedigree drawing / management / modelling (teaching, research, and family-history documentation)

## What Evagene Does

- Draw family pedigrees using standard clinical genetic notation (ISCN/HGNC) on an HTML5 canvas with gesture drawing or keyboard shortcuts
- Capture a family and personal health history through a guided, step-by-step questionnaire (family history intake) that turns the answers into a pedigree — creating relatives, relationships, the proband, and recorded conditions automatically; educational data capture, not a medical assessment, and it produces no risk output
- Annotate individuals with diseases, genetic tests, clinical tests, treatments, allergies, traits, and ancestry
- Run integrated Bayesian cancer risk models: BRCAPRO (breast/ovarian), MMRpro (Lynch syndrome), PancPRO (pancreatic)
- Run Mendelian inheritance risk models: autosomal dominant, autosomal recessive, X-linked recessive
- Run X-linked dominant models with five sex-differential severity sub-modes: equal, males-worse, male-lethal-reproduces (1:1:1 live-born ratio for incontinentia pigmenti / focal dermal hypoplasia / OFD1), male-lethal-no-reproduction (Rett syndrome / MECP2 / CDKL5), and metabolic-interference males-unaffected (CFND / EFNB1, EFMR / PCDH19)
- Run mitochondrial (mtDNA) models with strict maternal transmission, sex-differential penetrance, and heteroplasmy scaling (LHON, MELAS, MERRF, NARP, Leigh mtDNA subset, Kearns-Sayre, Pearson)
- Run digenic two-locus interaction models with the classical 25% offspring-affected ratio (Usher syndrome type 2, some retinitis pigmentosa, primary congenital glaucoma); supports both_het / one_het_one_hom / both_hom configurations
- Run imprinting / uniparental disomy models with mechanism-weighted recurrence risk (deletion, UPD, imprinting-centre defect, point mutation) and the parent-of-origin rule for IC defects (Prader-Willi, Angelman, Beckwith-Wiedemann, Silver-Russell, TNDM)
- Run polygenic / oligogenic / multifactorial recurrence-risk analysis via a liability-threshold engine (Carter 1961, Falconer 1965, Reich/James/Morton 1972), with empirical Smith / Carter / Harper tables and four classical counselling modifiers (severity, Carter-effect sex bias, multiple affected relatives, parental consanguinity)
- Surface population-conditioned carrier priors across the AR / XLR catalogue, weighted by the individual's recorded ancestry proportions. Each row attributes its number to one of three sources: explicit population key (direct published carrier frequency), weighted mix (proportion-weighted combination for mixed ancestry), or Hardy-Weinberg estimate from incidence (2pq). Ancestry-gated by default: no carrier number is shown for an individual without recorded ancestry — closing the common clinical-tool failure mode of presenting a "general population" figure as applying to a specific person.
- Run cancer family-history scoring: Claus (CASH), Couch BRCA1 logistic, Frank/Myriad empirical BRCA1+BRCA2, Manchester Scoring System (Evans 2004), NICE CG164/NG101 categorisation, Amsterdam II Lynch-syndrome criteria (Vasen 1999), Revised Bethesda (Umar 2004), Gail NCI BCRAT (Gail 1989), an educational prostate-cancer family-history risk model (illustrative), and a Tyrer-Cuzick IBIS-style approximation of the Tyrer/Duffy/Cuzick 2004 algorithm (clearly labelled in-app as an approximation, not the official IBIS binary)
- Export BOADICEA v4 / CanRisk v2 pedigree files for upload at canrisk.org (BOADICEA is not bundled; licensed by the University of Cambridge)
- AI-assisted draft summaries for educational / research review: structural observations, family-structure notes, documentation gaps, and discussion prompts linked to published literature — not clinical advice, not diagnostic output
- Auto-generate pedigree description reports in structured English
- Catalogue of 230+ genetic diseases cross-referenced to ICD-10, OMIM, MONDO, Orphanet, and Disease Ontology (DOID) identifiers, with inheritance parameters (includes 20+ catalogued multifactorial / polygenic / oligogenic conditions with heritability and empirical recurrence risks)
- HPO phenotyping: browse and search a curated Human Phenotype Ontology catalogue and attach observed or excluded phenotype features (with onset and severity) to individuals — educational reference data and data entry, not a medical assessment
- Phenotype-to-gene educational associations: from an individual's recorded HPO features, surface candidate associated genes as educational associations (reference data like Related concepts — candidate associations only, never a ranked likelihood, no diagnosis, no recommendation)
- Relatedness / IBD analysis: full pairwise kinship coefficients, per-individual inbreeding, Jacquard condensed identity / expected genome-wide IBD sharing (k0/k1/k2), and a gene-dropping relatedness simulation — educational / research, never forensic
- Disease management dashboard with search, taxonomy views, presets, and custom colours
- Related concepts: a hand-curated educational correlation graph (1,100+ curated associations plus auto-derived genetic edges) linking diseases, traits, clinical-test results, allergies, and markers, surfaced in the editor's Related concepts panel and via the open /api/correlations endpoints and the MCP related_concepts tool. Eight relationship types (biomarker, associated_finding, associated_condition, shares_features, sequela, risk_association, genetic_association, shared_gene); status-qualified clinical-test edges (e.g. low vs high ferritin). Educational reference data — not risk analysis, not diagnosis, asserts nothing about any person
- 55+ allergies and 50+ traits with genetic marker associations
- Blood type (ABO, Rh) and secretor status inference from 23andMe SNP markers
- Interactive karyogram viewer with hover tooltips, click-to-pin info panels, and canvas embedding
- Consanguinity detection with Wright's coefficient calculation
- Ancestry management with auto-calculation
- Advanced search and filtering across pedigree data
- Import: JSON, GEDCOM 5.5.1, GA4GH Phenopackets v2, 23andMe (genotype, traits, health history), XEG (legacy), pedigree images (OCR), and the Evagene Pedigree Builder ChatGPT Custom GPT — describe a family in plain English and get back an importable JSON file (Route A; paid ChatGPT tier required)
- Export: JSON, GEDCOM, GA4GH Phenopackets v2, PNG, SVG, PDF, DOCX
- Batch risk screening: screen a proband across all diseases simultaneously with configurable thresholds
- Four educational report types: plain-language summary, structured summary, carrier probability, and AI-generated draft summary — all for educational / research review, not medical advice
- Anchored canvas notes that follow individuals when moved
- Rich text editing with markdown formatting and live preview
- Pedigree duplication and improved twin/pregnancy management

## Who It's 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 (clinicians, counsellors) are addressed as educators, researchers, and learners, not as operators of a clinical-workflow tool.

- Researchers in clinical and medical genetics
- Educators and students (medical, nursing, biology, genetic counselling)
- Genetic counsellors (for teaching, training, and structured documentation)
- Clinical geneticists (for teaching, research, and structured family-history documentation)
- Oncologists, general practice doctors, and genetic nurses (for documentation, teaching, and reference)
- Genealogists and family-history researchers
- Patients and families (for personal family-history documentation and self-education — not medical advice)

## Help & Documentation

Comprehensive documentation is available at https://evagene.net/help with 1,900+ individual help guides across six catalogues:
- Diseases (230+, ICD-10 + OMIM)
- Traits (heritability, marker associations)
- Allergies (IgE status, cross-reactivity)
- Clinical tests (LOINC-linked)
- Markers / genes (NCBI Gene, OMIM, ClinVar)
- Treatments (RxNorm, BNF, DrugBank)

Also: introductory / intermediate / advanced genetics guides, role-specific workflow guides for 8 professional groups, risk model documentation (BRCAPRO, MMRpro, PancPRO, Claus, Couch, Frank, Manchester, NICE, Amsterdam II, Bethesda, Gail, Tyrer-Cuzick approximation, CanRisk export, Mendelian + non-classical models, polygenic liability-threshold), and a keyboard shortcut reference.

Browse the catalogue at https://evagene.net/help/#browse — or jump straight to clinical tests (https://evagene.net/help/#clinical-tests), markers / genes (https://evagene.net/help/#markers), or treatments (https://evagene.net/help/#treatments).

## User Guide (Getting Started)

A click-by-click getting-started guide organised around the editor's dock, with a worked example on every page. Written for users who know the genetics but are new to Evagene. Index: https://evagene.com/user-guide/

- Canvas basics — add, select, connect individuals; undo / redo / find: https://evagene.com/user-guide/canvas-basics
- View & layout — grid, zoom, font, dark mode, auto-arrange: https://evagene.com/user-guide/view-and-layout
- Pedigree builder — drag-and-drop family construction: https://evagene.com/user-guide/pedigree-builder
- Family history questionnaire — guided step-by-step intake that turns answers into a pedigree (educational data capture, not a medical assessment): https://evagene.com/user-guide/family-history
- Individual properties — identity, clinical status, dates, consent: https://evagene.com/user-guide/individual-properties
- Pedigree & relationship properties — pedigree settings, consanguinity, events: https://evagene.com/user-guide/pedigree-properties
- Family register — sortable grid view: https://evagene.com/user-guide/family-register
- Files — import, export, image / PDF / DOCX, 23andMe: https://evagene.com/user-guide/files/
- Disease catalogue — add diseases and record them on individuals: https://evagene.com/user-guide/diseases
- Investigations Manager (formerly Tests Manager) — clinical test types and results: https://evagene.com/user-guide/investigations
- Interventions — treatment tracking: https://evagene.com/user-guide/interventions
- Genetics — markers, karyogram, karyotype, ancestry: https://evagene.com/user-guide/genetics/
- Related concepts — educational correlation graph: https://evagene.com/user-guide/related-concepts
- Risk analysis — illustrative / educational risk models (single-gene & liability, cancer family-history scores & Tyrer-Cuzick approximation, BayesMendel, CanRisk / BOADICEA export): https://evagene.com/user-guide/risks/

## Platform & Integrations

Evagene includes a platform layer for programmatic access and third-party integration:

- REST API with scoped, rate-limited API keys (format: evg_<43 chars>, SHA-256 hashed at rest, read/write/analyse scopes)
- Bring Your Own Key (BYOK) LLM support for Anthropic (Claude) and OpenAI (GPT), encrypted at rest with Fernet
- Webhooks with HMAC-SHA256 signed payloads for 8 event types (pedigree/individual CRUD, analysis completed, import completed)
- Analysis Templates: reusable custom AI prompt templates with variable injection ({{pedigree_description}}, {{proband_name}}, etc.)
- MCP Server: 27 tools via the Model Context Protocol for Claude Desktop, Claude Code, and other AI agents (incl. disease-ontology lookup, HPO term browse, phenotype attach, phenotype-to-gene, Phenopackets import/export, and relatedness coefficients)
- Embeddable Pedigree Viewer: iframe, raw SVG, or JavaScript snippet for patient portals, research dashboards, and EHR integration

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.

## Genetic Current — daily genetics news

- [Genetic Current](https://evagene.com/news/) — A daily-updated news section summarising public-source genetics and genomics reporting for researchers, clinicians, educators, students, genealogists, and patients. Stories are AI-drafted educational summaries of items from ~16 trusted public sources (NHGRI, CDC Genomics, NHS England, Genomics England, PHG Foundation, Wellcome Sanger, Cancer Research UK, The Conversation, PLOS Genetics, Nature Medical Genetics, EurekAlert, ScienceDaily, Stat News, The Scientist, bioRxiv preprints) clustered to one canonical story per finding, with audience tags and an optional plain-language "for patients" version. Trending is computed by cross-source consensus rather than engagement metrics. Each story links to its original public sources. Educational and research use only — not medical advice.
- 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/).
- [Archive](https://evagene.com/news/archive/) — by month.

## Release Notes

- [17 April 2026 — Polygenic, cancer family-history, and CanRisk export](https://evagene.com/release-2026-04-risk-expansion.html) — Release notes for the liability-threshold engine (Carter 1961, Falconer 1965), nine new cancer family-history scoring models (Claus, Couch, Frank, Manchester, NICE CG164/NG101, Amsterdam II, Bethesda, Gail, Tyrer-Cuzick IBIS-style approximation), and one-click CanRisk / BOADICEA v4 pedigree export. Cites canonical papers for every model. BOADICEA is not bundled (licensed by University of Cambridge); Tyrer-Cuzick output is clearly labelled as an approximation.
- [18 April 2026 — X-linked dominant, mitochondrial, digenic, imprinting / UPD](https://evagene.com/release-2026-04-18-inheritance-patterns.html) — Four additional inheritance models for clinical geneticists, genetic counsellors, and reproductive medicine. XLD with five sex-differential severity sub-modes (Rett-class, incontinentia pigmenti, CFND, EFMR). Mitochondrial with maternal transmission and heteroplasmy scaling (LHON, MELAS, MERRF, NARP, Leigh, Kearns-Sayre, Pearson). Digenic with classical 25% ratio (Usher type 2, some RP, primary congenital glaucoma). Imprinting / UPD with mechanism-weighted recurrence and parent-of-origin rule (Prader-Willi, Angelman, Beckwith-Wiedemann, Silver-Russell, TNDM).
- [27 May 2026 — Related Concepts (educational correlation graph)](https://evagene.com/release-2026-05-27-related-concepts.html) — A hand-curated correlation graph (1,100+ curated associations) plus auto-derived genetic edges (genetic_association, shared_gene) linking diseases, traits, clinical-test results, allergies, and markers, surfaced in the editor's Related concepts panel. Status-qualified clinical-test edges (low vs high ferritin). Available via the open /api/correlations endpoints and a related_concepts MCP tool (the server now has 27 tools). Educational reference data — not risk analysis, not diagnosis, asserts nothing about any person.
- [Complex-disease pedigree software](https://evagene.com/complex-disease-pedigree-software.html) — The 20+ catalogued multifactorial / polygenic / oligogenic conditions with filter and links to per-condition in-app help guides.

## Topic Guides

- [Everything Evagene Does — Complete Feature List](https://evagene.com/features.html) — single-page catalogue of every capability: gesture drawing and NSGC notation, guided family-history intake, the 230+ disease catalogue, twenty-one published risk-model algorithms, HPO phenotyping, the related-concepts graph, consanguinity and IBD, AI-assisted draft summaries, GEDCOM / Phenopackets / CanRisk interoperability, the platform layer (REST API, BYOK LLM, webhooks, analysis templates, 27-tool MCP server, embeddable viewer), and 25 open-source MIT integration examples
- [Pedigree Drawing Tool](https://evagene.com/pedigree-drawing-tool.html) — 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) — Definitional pillar: symbols, three-generation capture, inheritance patterns visible in a pedigree
- [Clinical Pedigree Drawing](https://evagene.com/clinical-pedigree-drawing.html) — 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) — Complete guide to pedigree drawing, standard notation, and pedigree software comparison
- [Pedigree Chart Maker](https://evagene.com/pedigree-chart-maker.html) — Free in-browser NSGC-compliant chart maker
- [Pedigree Drawing Online](https://evagene.com/pedigree-drawing-online.html) — Browser-based pedigree drawing with no install
- [Clinical Pedigree Drawing Guidelines](https://evagene.com/clinical-pedigree-drawing-guidelines.html) — NSGC 1995, 2008, and 2022 standards, plus ISCN, HGNC, HPO context
- [Hereditary Cancer Risk Assessment](https://evagene.com/hereditary-cancer-risk-assessment.html) — BRCAPRO, MMRpro, PancPRO, and Bayesian cancer risk modelling
- [GEDCOM & Genealogy](https://evagene.com/gedcom-pedigree-software.html) — GEDCOM import/export, 23andMe integration, and genealogy interoperability
- [Clinical Genetics Pedigree Tool](https://evagene.com/clinical-genetics-pedigree-tool.html) — Pedigree software for clinical geneticists and genetic counsellors
- [Mendelian Inheritance Calculator](https://evagene.com/mendelian-inheritance-calculator.html) — Autosomal dominant, autosomal recessive, and X-linked inheritance models
- [Platform & Integrations](https://evagene.com/platform.html) — API keys, BYOK LLM, webhooks, analysis templates, MCP server, embeddable viewer
- [Related Concepts Explorer](https://evagene.com/related-concepts-explorer.html) — the educational correlation graph linking diseases, traits, clinical-test results, allergies, and markers; two edge sources (curated + marker-derived), eight relationship types, status-qualified test edges, the Related concepts editor panel, and /api/correlations + MCP related_concepts access. Not risk analysis, not diagnosis
- [Biomarker & Condition Associations](https://evagene.com/biomarker-disease-associations.html) — status-qualified clinical-test edges (low vs high), the biomarker / associated-finding / risk-association relationships, worked through the iron studies (ferritin, transferrin saturation, MCV). Educational reference, not diagnosis
- [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 across diseases, traits, tests, allergies, and genes (pleiotropy, lab panels, associated conditions). Educational, not clinical
- [Pedigree Builder GPT](https://evagene.com/pedigree-builder-gpt.html) — ChatGPT Custom GPT that converts a plain-English family description into an Evagene-compatible pedigree JSON file. Route A (produces a file the user loads at evagene.net); Route B (live Evagene API Actions) planned but not yet built. Paid ChatGPT subscription required (OpenAI's policy for all Custom GPTs). Live at https://chatgpt.com/g/g-69ea28b554b8819191ae0f8fd2406d52-evagene-pedigree-builder

## Learning Hub

- [Learn Genetics — reading pathways](https://evagene.com/learn-genetics.html) — Microsoft-Learn-style pathway page that organises the 46 educational pages plus the 20 risk-model calculators into seven structured reading pathways: Foundations (genetics from scratch), Molecular biology deep dive, Clinical genetics, Cancer genetics, Population & quantitative, Therapeutics & gene therapy, and Refresher (recent advances). 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 working calculators and the pedigree drawing tool. Free in the browser, no registration, no paywall.

## Free Embeds

- [Embed pedigree drawing — free iframe](https://evagene.com/embed-pedigree-drawing.html) — drop-in iframe (`https://evagene.net/draw`) for any website, blog, course page, LMS module, or app. Visitors get the full Evagene pedigree drawing canvas: gesture drawing, NSGC notation, disease annotation against the 1,900-entry catalogue, exports (PDF, PNG, SVG, GEDCOM, CanRisk, Phenopackets v2). No install, no signup, no API key. 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) — read-only display embed for an existing pedigree fetched from Evagene; iframe / raw SVG / JavaScript snippet modes; suits research dashboards and public-pedigree research figures.

## Interactive Visualisation

- [Evanthe — an interactive Galaxy of Life](https://evagene.com/evanthe/) — a free, browser-based 3D Galaxy of Life by Evagene. Drift through the branches of taxonomic classification (domain → kingdom → phylum → class → order → family → genus), search living things, and explore how life is organised. A playful educational visualisation and standalone toy, not part of the pedigree platform; no install, no signup.

## Educational Topics

A curated set of educational landing pages on the molecular, clinical, and population-genetics topics taught at MSc / FRCPath / equivalent level. Each page is a 1,300–2,000-word survey with citations to peer-reviewed papers, NCBI / OMIM / GeneReviews entries, and standards-body resources. Framed throughout as 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, supercoiling, nucleosomes, TADs
- [DNA Replication and Repair](https://evagene.com/dna-replication-and-repair.html) — replisome, polymerases, MMR, NER, BER, HR, NHEJ
- [Genome Structure and Variation](https://evagene.com/genome-structure-and-variation.html) — repetitive DNA, transposons, CNV, structural variant detection

### Gene Expression Mechanisms
- [Gene Expression Mechanisms](https://evagene.com/gene-expression-mechanisms.html) — pillar
- [Transcriptional Machinery](https://evagene.com/transcriptional-machinery.html) — Pol I/II/III, CTD cycle, promoters, enhancer-promoter contact
- [RNA Processing and Stability](https://evagene.com/rna-processing-and-stability.html) — spliceosome, alternative splicing, polyadenylation, NMD
- [Translation and Post-Translational Control](https://evagene.com/translation-and-post-translational-control.html) — ribosome, eIFs, ribosome profiling, chaperones, PTMs

### Regulation of Gene Activity
- [Regulation of Gene Activity](https://evagene.com/regulation-of-gene-activity.html) — pillar
- [Cis and Trans Regulatory Elements](https://evagene.com/cis-and-trans-regulatory-elements.html) — enhancers, silencers, insulators, super-enhancers, ChIP-seq, ATAC-seq, eQTLs
- [Epigenetics and Chromatin Dynamics](https://evagene.com/epigenetics-and-chromatin-dynamics.html) — DNA methylation, histone marks, ChromHMM, Polycomb, X-inactivation, TADs, loop extrusion
- [Gene Regulatory Networks](https://evagene.com/gene-regulatory-networks.html) — network motifs, miRNAs, lncRNAs, Perturb-seq

### Mutation Biology and Consequences
- [Mutation Biology and Consequences](https://evagene.com/mutation-biology-and-consequences.html) — pillar
- [Types of Mutation](https://evagene.com/types-of-mutation.html) — point mutations, indels, repeat expansions, mutational signatures
- [Functional Consequences of Mutation](https://evagene.com/functional-consequences-of-mutation.html) — LoF, gain-of-function, dominant negative, splice and regulatory mutations
- [Mutation Detection and Interpretation](https://evagene.com/mutation-detection-and-interpretation.html) — NGS, ACMG/AMP framework, in silico predictors

### Chromosomes and Cell Division
- [Chromosomes and Cell Division](https://evagene.com/chromosomes-and-cell-division.html) — pillar
- [Chromosome Structure and Mapping](https://evagene.com/chromosome-structure-and-mapping.html) — centromeres, telomeres, banding, FISH, T2T-CHM13
- [Cell Cycle, Mitosis, Meiosis](https://evagene.com/cell-cycle-mitosis-meiosis.html) — cyclin-CDK, checkpoints, recombination, PRDM9
- [Chromosomal Abnormalities](https://evagene.com/chromosomal-abnormalities.html) — aneuploidy, structural rearrangements, microdeletion / microduplication syndromes

### Mendelian Genetics and Gene Discovery
- [Mendelian Genetics and Gene Discovery](https://evagene.com/mendelian-genetics-and-gene-discovery.html) — pillar
- [Inheritance Patterns](https://evagene.com/inheritance-patterns.html) — autosomal dominant / recessive, X-linked, mitochondrial, imprinting
- [Pedigree Analysis and Variable Expression](https://evagene.com/pedigree-analysis-and-variable-expression.html) — penetrance, expressivity, mosaicism, Bayesian risk calculation
- [Mapping and Gene Identification](https://evagene.com/mapping-and-gene-identification.html) — linkage, GWAS, exome / WGS, Matchmaker Exchange

### Quantitative and Complex Traits
- [Quantitative and Complex Traits](https://evagene.com/quantitative-and-complex-traits.html) — pillar
- [Polygenic Models](https://evagene.com/polygenic-models.html) — Fisher's infinitesimal model, polygenic risk scores, PGS Catalog, portability
- [Heritability and Liability](https://evagene.com/heritability-and-liability.html) — twin / SNP heritability, GREML, LDSC, Falconer threshold model, Carter effect
- [Gene-Environment Interaction](https://evagene.com/gene-environment-interaction.html) — GxE designs, Mendelian randomisation, epigenetic mediation

### Population and Evolutionary Genetics
- [Population and Evolutionary Genetics](https://evagene.com/population-and-evolutionary-genetics.html) — pillar
- [Allele Frequency Dynamics](https://evagene.com/allele-frequency-dynamics.html) — Hardy-Weinberg, selection, drift, neutral theory
- [Demography and Population Structure](https://evagene.com/demography-and-population-structure.html) — F-statistics, PCA, ADMIXTURE, founder effects
- [Population Genetics Applications](https://evagene.com/population-genetics-applications.html) — carrier-screening epidemiology, Wilson-Jungner criteria, ELSI

### Haemoglobin and Development
- [Haemoglobin and Development Genetics](https://evagene.com/haemoglobin-and-development-genetics.html) — pillar
- [Haemoglobin Biology and Disorders](https://evagene.com/haemoglobin-biology-and-disorders.html) — HbA / HbF / HbA2, sickle cell, α- and β-thalassaemia, Casgevy / exa-cel
- [Genes in Development](https://evagene.com/genes-in-development.html) — WNT, SHH, Notch, BMP/TGF-β, FGF, Hippo, RASopathies, FGFR3 dysplasia series

### Cancer Genetics and Somatic Variation
- [Cancer Genetics and Somatic Variation](https://evagene.com/cancer-genetics-and-somatic-variation.html) — pillar
- [Oncogenes and Tumour Suppressors](https://evagene.com/oncogenes-and-tumour-suppressors.html) — Knudson two-hit, RAS/MYC/BCR-ABL/HER2/EGFR/BRAF, gatekeeper / caretaker / landscaper
- [Inherited Cancer Predisposition](https://evagene.com/inherited-cancer-predisposition.html) — HBOC, Lynch, FAP, MAP, Li-Fraumeni, Cowden, Peutz-Jeghers, HDGC, VHL, MEN1/2, NF1/2, TSC, retinoblastoma
- [Somatic Genomics](https://evagene.com/somatic-genomics.html) — clonal evolution, mutational signatures, HRD, MSI, TMB, targeted-therapy biomarkers

### Metabolic Genetics and Therapeutics
- [Metabolic Genetics and Therapeutics](https://evagene.com/metabolic-genetics-and-therapeutics.html) — pillar
- [Inborn Errors of Metabolism](https://evagene.com/inborn-errors-of-metabolism.html) — Garrod, pathway-block reasoning, NBS, IEM categories
- [Pharmacogenetics and Precision Therapy](https://evagene.com/pharmacogenetics-and-precision-therapy.html) — CYP polymorphisms, HLA-B*57:01, CPIC, gene therapy, CRISPR / base / prime editing

### Clinical Practice, Ethics, and Communication
- [Clinical Practice, Ethics, and Communication](https://evagene.com/clinical-practice-ethics-communication.html) — pillar
- [Clinical Genetic Skills](https://evagene.com/clinical-genetic-skills.html) — structured family-history interview, three-generation pedigree, NSGC 2022, dysmorphology
- [Diagnostics and Counselling](https://evagene.com/diagnostics-and-counselling.html) — test taxonomy, ACMG/AMP, secondary findings, Reciprocal-Engagement Model, cascade testing
- [Ethics, Legal and Social Issues](https://evagene.com/ethics-legal-social-issues.html) — NHGRI ELSI, GINA, GDPR, duty-to-warn, equity in genomics, polygenic embryo selection

## Comparisons & Alternatives

Honest side-by-side and alternatives guides for every major clinical pedigree platform. Claims about competitors are drawn from their public websites as of April 2026.

- [Compare Evagene](https://evagene.com/compare.html) — hub listing every Evagene-vs-X comparison
- [Alternatives field guides](https://evagene.com/alternatives.html) — "alternatives-to-X" guides (Phenotips, Progeny, TrakGene, FamGenix, CanRisk, GenoPro, PedigreeTool, QuickPed)
- [BOADICEA vs BRCAPRO](https://evagene.com/boadicea-vs-brcapro.html) — the two leading BRCA risk models compared honestly
- [IBIS (Tyrer-Cuzick) vs Evagene](https://evagene.com/ibis-tyrer-cuzick-vs-evagene.html) — the official, validated IBIS Breast Cancer Risk Evaluator (Tyrer-Cuzick, QMUL) vs Evagene's IBIS-style approximation inside a research and education pedigree platform; use the official tool for definitive numbers
- [pedigreejs vs Evagene](https://evagene.com/pedigreejs-vs-evagene.html) — the Cambridge CCGE/BOADICEA team's open-source, embeddable pedigree editor (CanRisk export) vs a full pedigree platform with risk models, AI agents, and catalogues
- [CancerIQ vs Evagene](https://evagene.com/canceriq-vs-evagene.html) — a clinical EHR-integrated hereditary-cancer workflow platform vs Evagene, a research and education pedigree tool (not a medical device)
- [Lucidchart vs Evagene](https://evagene.com/lucidchart-pedigree-vs-evagene.html) — general diagramming with genogram templates vs a genetics-aware pedigree platform

## Best-of Guides

- [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 hereditary cancer risk tools](https://evagene.com/best-hereditary-cancer-risk-tools.html)
- [Best clinical genetics software](https://evagene.com/best-clinical-genetics-software.html)

## Risk & Inheritance Calculators

- [BRCAPRO calculator](https://evagene.com/brcapro-calculator.html) · [MMRpro](https://evagene.com/mmrpro-calculator.html) · [PancPRO](https://evagene.com/pancpro-calculator.html)
- [Lynch syndrome risk calculator](https://evagene.com/lynch-syndrome-risk-calculator.html)
- [Breast cancer family history calculator](https://evagene.com/breast-cancer-family-history-calculator.html) · [Ovarian](https://evagene.com/ovarian-cancer-family-history-calculator.html) · [Pancreatic](https://evagene.com/pancreatic-cancer-family-history.html)
- [Tyrer-Cuzick alternative](https://evagene.com/tyrer-cuzick-alternative.html) · [BOADICEA alternative](https://evagene.com/boadicea-alternative.html)
- [Autosomal dominant](https://evagene.com/autosomal-dominant-calculator.html) · [Autosomal recessive](https://evagene.com/autosomal-recessive-calculator.html) · [X-linked recessive](https://evagene.com/x-linked-recessive-calculator.html)
- [Carrier probability](https://evagene.com/carrier-probability-calculator.html) · [Consanguinity / Wright's coefficient](https://evagene.com/consanguinity-calculator.html)
- [Inheritance pattern identifier](https://evagene.com/inheritance-pattern-identifier.html)
- [Germline mosaicism calculator](https://evagene.com/germline-mosaicism-calculator.html) — parental mosaicism posterior from pedigree structure plus optional somatic VAF, with joint-parent logic

## Condition-Specific Pedigree Guides

- [Duchenne muscular dystrophy pedigree](https://evagene.com/duchenne-muscular-dystrophy-pedigree.html)
- [Dravet syndrome pedigree](https://evagene.com/dravet-syndrome-pedigree.html)
- [Rett syndrome pedigree](https://evagene.com/rett-syndrome-pedigree.html)
- [Osteogenesis imperfecta pedigree](https://evagene.com/osteogenesis-imperfecta-pedigree.html)
- [Achondroplasia pedigree](https://evagene.com/achondroplasia-pedigree.html)
- [Tuberous sclerosis pedigree](https://evagene.com/tuberous-sclerosis-pedigree.html)

## For Specific Users

- [For clinical geneticists](https://evagene.com/for-clinical-geneticists.html)
- [For genetic counsellors](https://evagene.com/for-genetic-counsellors.html)
- [For reproductive medicine](https://evagene.com/for-reproductive-medicine.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)

## Inheritance-Model Landing Pages

- [Mitochondrial inheritance pedigree software](https://evagene.com/mitochondrial-inheritance-pedigree.html) — LHON, MELAS, MERRF, NARP, Leigh (mtDNA subset), Kearns-Sayre, Pearson. Strict maternal transmission, sex-differential penetrance, heteroplasmy scaling.
- [X-linked dominant pedigree software](https://evagene.com/x-linked-dominant-pedigree.html) — five sex-differential severity sub-modes (equal, males-worse, male-lethal-reproduces for incontinentia pigmenti / OFD1, male-lethal-no-reproduction for Rett-class, metabolic-interference males-unaffected for CFND / EFMR).
- [Digenic inheritance pedigree software](https://evagene.com/digenic-inheritance-pedigree.html) — two-locus interaction with the classical 25% offspring-affected ratio; Usher syndrome type 2, some retinitis pigmentosa, primary congenital glaucoma.
- [Imprinting &amp; UPD pedigree software](https://evagene.com/imprinting-upd-pedigree.html) — mechanism-weighted recurrence (deletion / UPD / IC defect / point mutation) and parent-of-origin rule for Prader-Willi, Angelman, Beckwith-Wiedemann, Silver-Russell, TNDM.

## Platform & Developer Guides

- [Pedigree REST API](https://evagene.com/pedigree-api.html) · [Webhooks & events](https://evagene.com/platform.html)
- [Pedigree MCP server (Claude Desktop, Claude Code)](https://evagene.com/pedigree-mcp-server.html)
- [LLM pedigree analysis with BYOK](https://evagene.com/llm-pedigree-analysis.html)
- [Embeddable pedigree viewer](https://evagene.com/embeddable-pedigree-viewer.html)
- [HL7 FHIR pedigree](https://evagene.com/hl7-fhir-pedigree.html) · [EHR integration](https://evagene.com/ehr-pedigree-integration.html)
- [GEDCOM to pedigree converter](https://evagene.com/gedcom-to-pedigree-converter.html) · [Phenopackets](https://evagene.com/phenopackets-pedigree.html)

## Notation & Tutorial References

- [How to draw a pedigree chart](https://evagene.com/how-to-draw-a-pedigree-chart.html) · [5 simple steps](https://evagene.com/pedigree-chart-5-steps.html)
- [Pedigree symbols reference](https://evagene.com/pedigree-symbols-reference.html) · [Pedigree chart examples](https://evagene.com/pedigree-chart-examples.html)
- [NSGC pedigree notation](https://evagene.com/nsgc-pedigree-notation.html) · [ISCN pedigree symbols](https://evagene.com/iscn-pedigree-symbols.html) · [Standard pedigree nomenclature](https://evagene.com/standard-pedigree-nomenclature.html)
- [Three-generation family history](https://evagene.com/three-generation-family-history.html) · [Gender-inclusive pedigree drawing](https://evagene.com/gender-inclusive-pedigree-drawing.html)

## Specialised & Country 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 risk screening](https://evagene.com/batch-pedigree-risk-screening.html)
- [Genogram vs pedigree](https://evagene.com/genogram-vs-pedigree.html) · [Medical genogram software](https://evagene.com/medical-genogram-software.html)
- [23andMe pedigree import](https://evagene.com/23andme-pedigree-import.html) · [Medical family tree](https://evagene.com/medical-family-tree.html) · [Family health history online](https://evagene.com/family-health-history-online.html)
- [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)

## Optional

- [Full documentation](https://evagene.com/llms-full.txt)
- [XML sitemap](https://evagene.com/sitemap.xml) — complete list of all indexable pages