f-tree vs Evagene: a detailed pedigree software comparison

Short version. f-tree is a pedigree-charting application developed jointly by Iwate Medical University and Holonic Systems in Japan. Its earlier form, f-treeGC, was published in BMC Medical Genetics in 2017, which gives it a rare thing in pedigree software: a peer-reviewed methodology paper. It is a desktop and mobile product (Windows, macOS, iPad, iPhone), centred on questionnaire-driven automatic pedigree generation, and it has been used in heredity clinics, genome cohort studies, and even secondary-education contexts. Evagene is a cloud-native, browser-based clinical pedigree platform with integrated BayesMendel risk models, AI clinical interpretation via bring-your-own-key (BYOK) LLMs, a REST API, webhooks, an MCP server for AI agents, and an embeddable pedigree viewer. The two products are respectable fits for different deployment philosophies: f-tree for institutions that prefer native desktop and mobile applications with an academic lineage; Evagene for teams that want modern web tooling and programmatic access.

This is an honest comparison. Where f-tree is stronger, we say so. Where Evagene is stronger, we say that too. f-tree claims are drawn from its Holonic Systems product pages, the 2017 BMC Medical Genetics paper, and public materials as of April 2026.

How the two products position themselves

f-tree is positioned as a serious, academically credible pedigree chart tool. Its headline strengths are its questionnaire-driven workflow — the tool auto-generates a pedigree as the user answers structured questions about family members — and its multi-platform native deployment. The BMC Medical Genetics publication establishes the product's methodology in the scholarly record, which matters for research settings and for clinics that like their tooling cited. Its use cases explicitly include heredity clinics, genome cohort studies, and educational programmes; the mobile versions make it attractive where tablets are the clinical device of choice.

Evagene is positioned as clinical-grade pedigree management for precision medicine, delivered as a browser application. Its focus is the pedigree as the central clinical artefact: gesture drawing for fast in-room construction, integrated BayesMendel risk models (BRCAPRO, MMRpro, PancPRO), Mendelian inheritance analysis, AI-powered clinical interpretation using the service's own LLM keys, and a platform layer (REST API, webhooks, MCP server, embeddable viewer, Analysis Templates) that makes pedigree data useful outside the application.

The headline shape difference: f-tree is a desktop and mobile native app grounded in academic work, with a questionnaire as its intake engine. Evagene is a cloud platform whose emphasis is the modern web stack — AI, API, programmable integration — with the pedigree as the data model at the centre.

Feature-by-feature comparison

The matrix below compares features each vendor publishes. A tick means the capability is publicly advertised; a dash means it is not publicly listed (which does not necessarily mean it is absent).

Matrix compiled from publicly available product pages, the BMC Medical Genetics 2017 paper, and marketing material as of April 2026. "—" indicates the capability is not publicly advertised and does not necessarily mean it is absent.

Deployment philosophy: desktop and mobile vs cloud

This is the cleanest axis of difference. f-tree deploys as native applications: Windows, macOS, iPad, iPhone. That gives it offline working, deep integration with the native file system, and a clinical experience that feels predictable on an iPad at the bedside or a desktop at the hospital workstation. It is a design choice with real benefits — no network dependency, no browser tab drift — and real costs: updates are install-managed, mobile and desktop clients must be kept in sync, and multi-user shared state depends on file-based exchange or an explicit server arrangement.

Evagene is cloud-native and browser-first. It runs in any modern browser on any modern device, including iPads, with zero install. Updates are continuous, the canvas is the same on every platform, and concurrent editing and sharing follow from being server-backed rather than file-based. The trade-off is the obvious one: offline working requires explicit design, and clinics without reliable connectivity may prefer a local client.

If your clinic is behind a restrictive network proxy, runs in a setting with unreliable internet, or has strong governance preferring locally-installed software, f-tree's deployment model is a genuine fit. If your service is already cloud-first for other clinical tools, Evagene's browser-based deployment removes an install management burden.

Pedigree construction: questionnaire vs gesture

f-tree's workflow emphasises questionnaire-driven auto-generation. A user (sometimes the patient, sometimes the clinician) answers structured questions about family members and the product draws the pedigree automatically. This is efficient and reduces clinician drawing time. It is particularly strong in genome cohort studies where a standardised questionnaire is the normal intake instrument.

Evagene's workflow is built around gesture drawing during live consultation: the clinician draws the pedigree while talking to the patient, using keyboard shortcuts and continuous gestures that automatically apply standardised symbols based on recorded sex and affected status. This matches a traditional genetic counselling style where the pedigree emerges in real time as the family story is told. Evagene does not ship a patient-completed intake questionnaire today; services wanting questionnaire-driven intake on Evagene would typically use a separate form tool and import the pedigree (or build the ingestion via the API).

The fit depends on where pedigree construction lives in your workflow: structured intake prior to consultation (f-tree) or live construction during consultation (Evagene).

Risk models, clinical analytics, and AI

f-tree's public materials focus on pedigree charting rather than integrated Bayesian risk modelling. It is an excellent chart maker, with academic credentials and multi-language support. Services whose workflow is "draw the pedigree, then run risk calculations separately in a different tool" will find f-tree perfectly serviceable for the drawing step.

Evagene integrates risk calculation directly on the pedigree data. BRCAPRO, MMRpro, and PancPRO run without re-entry; Mendelian inheritance calculators (AD, AR, XR) handle non-cancer monogenic analysis; and batch risk screening sweeps all catalogued diseases for a given proband, surfacing conditions whose family history crosses a risk or testing-eligibility threshold. Karyogram viewing and consanguinity detection (Wright's coefficient) are additional clinical analytics.

On AI, Evagene ships BYOK LLM interpretation: the clinician's service provides its own Anthropic Claude or OpenAI GPT key, which is encrypted at rest with Fernet, and clinical text flows to the model provider the service has already risk-assessed. Analysis Templates codify house style of report writing. The MCP server exposes 11 pedigree tools to Claude Desktop, Claude Code, and any other MCP-compatible AI agent, so a clinician can ask their AI assistant to read, modify, or analyse a pedigree from inside their normal AI workspace. None of this is f-tree's problem to solve — f-tree is explicitly a pedigree chart tool.

Interoperability and platform surface

f-tree, as a desktop and mobile native product, tends to exchange data via file export and import rather than network APIs. Whether GEDCOM or image export is available depends on the specific f-tree release; check current vendor documentation. For research use, file-based exchange can be entirely sufficient.

Evagene is platform-shaped. Its REST API uses scoped, rate-limited keys (format evg_ followed by 43 characters, SHA-256 hashed at rest). Webhooks deliver HMAC-SHA256-signed payloads across eight event types. The embeddable pedigree viewer ships as an iframe, SVG, or JavaScript snippet. Imports cover GEDCOM 5.5.1, JSON, 23andMe (SNP, traits, health), XEG, and pedigree images via OCR. Exports cover PNG, SVG, and PDF across 4 report types.

When to choose f-tree

• Your preference is for native desktop and mobile applications, not a browser-based product.
• Your workflow is questionnaire-driven and auto-pedigree generation from structured intake is central.
• You need Japanese-language interface support or operate in Japan.
• You value a peer-reviewed methodology published in BMC Medical Genetics (2017) as part of the product's credentials.
• You are running a genome cohort study or education programme where f-tree's established use fits.
• Your network or governance requires installed software rather than cloud.

When to choose Evagene

• You want browser-based deployment, zero install, and device-agnostic access.
• You draw pedigrees live during consultation and want gesture drawing optimised for that workflow.
• You need integrated cancer risk modelling (BRCAPRO, MMRpro, PancPRO) and Mendelian inheritance analysis directly on the pedigree.
• You want AI-assisted clinical interpretation using your own LLM keys (Anthropic, OpenAI), Analysis Templates for report drafting, and MCP tools for AI agents.
• You are building AI agents, internal tooling, or patient portals that need programmatic access via REST API, webhooks, or embeds.
• You want broad import coverage: GEDCOM 5.5.1, JSON, 23andMe, XEG, and pedigree image OCR.

Migrating from f-tree to Evagene

The practical path is GEDCOM or image. If your f-tree deployment exports GEDCOM 5.5.1 (check current version), that is the cleanest transfer into Evagene. If not, export the pedigree as an image and use Evagene's OCR import. Disease annotations should be mapped to ICD-10 and OMIM to match Evagene's catalogue. Questionnaire data that f-tree collected — if structured — can be transferred to Evagene's individual records via JSON import or the REST API.

For services running both tools in parallel during transition, the usual pattern is to continue f-tree for existing cases and start new cases in Evagene, migrating older pedigrees only when needed for clinical review.

Frequently asked questions

Related comparisons and reading

• Phenotips vs Evagene
• Progeny vs Evagene
• TrakGene vs Evagene
• Pedigree drawing software: a practical guide
• All Evagene comparisons
• Clinical genetics pedigree tools: a field guide