Progeny Cloud vs Evagene: free clinical pedigree software, honestly compared

Short version. Progeny Cloud is the free, cost-free cloud edition of Progeny Clinical — a product that has been in the hands of clinical geneticists since 1996 and is today owned by Ambry Genetics. It launched in 2015, runs on HIPAA-compliant cloud servers, intakes family history via a patient-completed questionnaire, and auto-generates a pedigree. If you are looking for the strongest free clinical pedigree tool from an established vendor and you are comfortable with a product whose vendor is a clinical laboratory, Progeny Cloud is a serious, credible option. Evagene is also free today, via an Alpha waiting list, but it is a different kind of product: a modern browser-first pedigree platform with gesture drawing, BayesMendel risk models, AI clinical interpretation via bring-your-own-key (BYOK) LLMs, a REST API, webhooks, and an MCP server for AI agents. Evagene is earlier-stage and more ambitious on tooling; Progeny Cloud is more conservative and more mature.

This page is an honest comparison. Where Progeny Cloud is stronger, we say so; where Evagene is stronger, we say that too. All Progeny Cloud claims here are drawn from its public pages and Progeny Genetics's own product documentation as of April 2026.

How the two products position themselves

Progeny Cloud (pedigree.progenygenetics.com) is marketed as the cost-free cloud version of Progeny's long-running clinical pedigree software. Its proposition is simple: you get a trusted, HIPAA-compliant, cloud-hosted pedigree application without a licence fee, with the expectation that you can upgrade to Progeny Clinical (paid) if your clinic grows and needs the advanced features, administrative controls, and vendor support that sit in the full product. Its intake workflow centres on a patient-facing Family History Questionnaire (FHQ), which auto-generates a pedigree that the clinician then refines. Since Ambry Genetics acquired Progeny, the free tier has continued to be offered, which is both generous and slightly double-edged: Ambry is itself a clinical diagnostic laboratory, and any software product owned by a lab is one whose long-term roadmap may be influenced by the parent company's testing business.

Evagene (evagene.com) is positioned as clinical-grade pedigree management for precision medicine, and it takes a platform-first approach: the pedigree is the central clinical artefact, drawn fast via gesture drawing during live consultation, and then surfaced through modern integration points — a REST API, webhooks, an MCP (Model Context Protocol) server with 11 tools for AI agents, and an embeddable pedigree viewer for portals and EHR shells. Its analytic surface is built around BayesMendel cancer risk models (BRCAPRO, MMRpro, PancPRO), Mendelian inheritance analysis, and AI-powered clinical interpretation using the service's own LLM keys, with those keys encrypted at rest using Fernet. The product is in Alpha; the waitlist is free.

The practical framing: Progeny Cloud is "free version of a mature clinical product owned by a lab", optimised for small clinics that want the trust of an established name without the contract. Evagene is "modern platform at its early stage, free during Alpha", optimised for teams who want AI, API, and programmatic access alongside traditional pedigree and risk features.

Feature-by-feature comparison

The matrix below compares features each vendor publishes on its public site or documentation. A tick means the feature is publicly advertised; a dash means it is not publicly listed (which does not necessarily mean absent — some enterprise capabilities are undisclosed).

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

Pedigree drawing and patient intake

The clearest workflow difference between the two products is how a pedigree comes into existence in the first place. Progeny Cloud was designed around the Family History Questionnaire (FHQ): the patient completes a structured questionnaire before or during the visit, and Progeny auto-generates a pedigree from the answers. The clinician then refines the drawing. For services whose volume is high and whose pedigree construction happens largely out-of-room — before consultation, via web form — this is an efficient pattern, and it is one of Progeny's genuine strengths.

Evagene takes a different route. Its pedigree canvas is built for live, in-room construction: gesture drawing lets the clinician keep the conversation going while the pedigree grows under their hands, with keyboard shortcuts and automatic symbol standardisation based on recorded sex and affected status. For clinicians who want to draw the pedigree as the patient talks — a classic counselling practice — this is the intended fit. Evagene does not currently ship a patient-completed questionnaire; services that want questionnaire-driven intake would need to pair Evagene with a separate intake form and either type the data in or import it.

Neither pattern is universally superior. The test is whether your service's pedigree typically appears before, during, or after the visit.

Risk models and clinical analytics

Progeny Cloud inherits cancer risk modelling from its Clinical parent product — the detail of which models, with which parameters, and at what sophistication, is not fully exposed on the public Cloud pages and in practice is gated in parts behind the paid tier. For a small clinic whose cancer risk workflow is modest, the Cloud edition's built-ins are usually adequate. For a service that needs the full suite (Tyrer-Cuzick, BOADICEA, PANELPRO, and so on) or specific model parameters, the Clinical edition is where that depth sits.

Evagene is explicit about its model coverage: BRCAPRO for breast and ovarian cancer, MMRpro for Lynch syndrome, and PancPRO for pancreatic cancer, all from the peer-reviewed BayesMendel suite, run directly on the pedigree without data re-entry. Beyond that, Evagene adds Mendelian inheritance calculators for autosomal dominant, autosomal recessive, and X-linked recessive patterns — useful in reproductive genetics and non-cancer monogenic settings where BayesMendel does not apply. A more unusual feature is batch risk screening: for a given proband, the software sweeps across all catalogued diseases, surfacing conditions whose family history crosses a risk or testing-eligibility threshold.

If your service is predominantly cancer genetics and you are comfortable with Progeny's opinions on which models to use, Progeny Cloud's integrated approach is fine. If you want to see exactly which model ran, on what inputs, with what outputs — and you want the same platform to cover monogenic non-cancer cases — Evagene's explicit model list and batch screening are closer to the ideal.

AI, API, and the modern integration surface

This is where the products diverge most. Progeny Cloud is a conventional clinical pedigree tool: canvas, forms, reports. It does not publicly advertise an AI clinical interpretation engine, a public REST API for third-party developers, webhooks, or an MCP server. Progeny Clinical (paid) has some enterprise integration capabilities at the institutional level, but these are not exposed in the free Cloud edition.

Evagene treats programmatic access as first-class. The REST API uses scoped, rate-limited keys (format evg_ followed by 43 characters, SHA-256 hashed at rest, with read/write/analyse scopes). Webhooks deliver HMAC-SHA256-signed payloads across eight event types (pedigree and individual create/update/delete, analysis completed, import completed). The MCP (Model Context Protocol) 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 directly from their normal AI workspace. And the embeddable pedigree viewer ships as an iframe, a raw SVG, or a JavaScript snippet, suitable for patient portals and research dashboards.

On AI, Evagene ships AI clinical interpretation that uses your own LLM keys (Anthropic Claude, OpenAI GPT), encrypted at rest with Fernet. Your clinical text flows to the model provider you have already risk-assessed — no Evagene-hosted model sits in the middle. Analysis Templates let a service codify its house style of report writing with variable injection ({{pedigree_description}}, {{proband_name}}) and reuse it across cases.

If your service will never want any of this, it is noise. If you expect AI-assisted drafting, patient-portal embedding, or building against an API to be part of your near-term work, the gap is large.

Vendor independence and lab-referral concerns

A practical consideration when choosing any free clinical software is who owns it and how that ownership shapes product decisions. Progeny Cloud is owned by Ambry Genetics, a US clinical diagnostic laboratory offering its own panels. There is no suggestion that Progeny Cloud steers ordering inappropriately, and the product long predated the Ambry acquisition. But clinics that want to avoid any perception that their pedigree tool is connected to a testing vendor — including services with institutional conflict-of-interest rules — may prefer an independent vendor.

Evagene is independent software, not owned by a laboratory. It does not bundle test ordering, and BYOK LLM support means even its AI layer goes to model providers of the service's own choosing. For some procurement committees this is a meaningful difference; for many clinics it is not a factor at all. Either way, it is worth knowing.

Interoperability and data portability

Progeny Cloud supports data export in some formats, but the Cloud tier is deliberately narrower than Progeny Clinical. If you intend to leave Progeny Cloud for another product later, check the specific export formats available in your account tier before committing.

Evagene supports GEDCOM 5.5.1 import and export, JSON, 23andMe (SNP, traits, and health imports), XEG (legacy pedigree format), and pedigree image OCR. PNG, SVG, and PDF export are available for reports and diagrams. The API and MCP server also provide programmatic access to the pedigree as structured data, which is the cleanest form of portability.

When to choose Progeny Cloud

• You want a free clinical pedigree tool from a long-established vendor and the fact that it is owned by Ambry Genetics is not a concern.
• Your workflow is patient-questionnaire-first: the Family History Questionnaire auto-generating a pedigree matches how your clinic actually runs.
• Your cancer-risk modelling needs are covered by Progeny's built-ins and you do not expect to need niche model configurations.
• You want a clear upgrade path to Progeny Clinical (paid) if your clinic grows.
• You do not anticipate needing AI, REST API, webhooks, MCP, or embeddable viewers in the near term.

When to choose Evagene

• You want to draw pedigrees live during consultation with gesture drawing and keyboard shortcuts.
• You want an explicit, auditable list of which cancer risk models run, on which inputs, with which outputs, plus Mendelian inheritance coverage for non-cancer monogenic cases.
• AI-assisted clinical interpretation matters, and you want to use your own LLM keys rather than rely on a vendor-chosen model.
• You are building AI agents, internal tooling, or patient portals that need programmatic pedigree access via REST API, webhooks, MCP, or an embeddable viewer.
• You want an independent vendor, not one owned by a clinical laboratory.
• You are willing to use Alpha software in exchange for modern tooling, and to give feedback on the product as it matures.

Migrating from Progeny Cloud to Evagene

If you decide to move from Progeny Cloud to Evagene, the route depends on what your Progeny Cloud account lets you export. GEDCOM export, where available, is the cleanest path into Evagene. If GEDCOM is not enabled on your tier, exporting pedigree images and using Evagene's OCR import is a viable fallback — less crisp than a structured export, but workable. Disease annotations that map to OMIM and ICD-10 transfer cleanly into Evagene's 200+ disease catalogue.

For clinics running both tools in parallel during transition, Evagene's REST API and webhooks allow a one-way sync to be built into the clinic's own integration layer if Progeny Cloud offers any programmatic export.

Frequently asked questions

Related comparisons and reading

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