QuickPed vs Evagene: relatedness analysis versus clinical pedigree management

Short version. QuickPed is a free, GPL3-licensed Shiny web app developed by Magnus D. Vigeland at the University of Oslo and published in BMC Bioinformatics 2022;23:220. It is genuinely excellent at what it sets out to do: kinship coefficients, inbreeding coefficients, identity coefficients, X-chromosomal variants, relatedness triangle visualisation, and a novel algorithm for describing pairwise relationships in natural language. It is aimed at researchers, case workers, and educators across medical, forensic, ecological and animal-breeding genetics. Evagene is a clinical-grade pedigree management system aimed at clinical genetics services, with integrated BayesMendel cancer risk models, a curated disease catalogue, AI-powered clinical interpretation, and a platform layer (REST API, webhooks, MCP, embeddable viewer). QuickPed and Evagene do different jobs, well. If your question is "how related are these two individuals, and what is the inbreeding coefficient?" then QuickPed is the right tool. If your question is "what should the clinical report on this family say, and how does the BRCAPRO risk look?" Evagene is the right tool. Many services will find a legitimate place for both.

This article is a careful, factual comparison. We are not trying to argue that Evagene replaces QuickPed — it does not, and it is not meant to. What we want to do is explain where each tool shines, so you can choose appropriately or use the two together. All claims about QuickPed are drawn from the published QuickPed paper, the manual, and the public Shiny deployment as of April 2026.

How the two products position themselves

QuickPed positions itself as a web-based interface to the pedsuite R packages — specifically a fast, browser-accessible way to build a pedigree and obtain rigorous relatedness statistics without writing R code. Its homepage describes it as a free, platform-independent tool for "case workers, researchers, and educators," and it is explicit about covering medical, forensic, ecology, and animal-breeding genetics use cases. Input is via a click-to-draw canvas or PED file import; output includes kinship and inbreeding coefficients, the full set of Jacquard's identity coefficients, X-chromosomal coefficient variants, an algorithmic description of the pairwise relationship between any two individuals (one of the paper's genuinely novel contributions), and R code that can be copied for reproducible downstream analysis. Built-in example pedigrees include historic royal families (Habsburg, Victoria, Tutankhamun) — a neat pedagogical touch and a good stress test of the underlying algorithms.

Evagene positions itself as clinical-grade pedigree management for precision medicine. Its emphasis is the clinical pedigree as a live working document: a gesture-drawing canvas for construction during consultation, standard NSGC/ISCN notation, a 200+ disease catalogue annotated with ICD-10 and OMIM codes, integrated BayesMendel cancer risk models (BRCAPRO, MMRpro, PancPRO), Mendelian inheritance calculators, AI-powered clinical interpretation using bring-your-own-key (BYOK) LLMs (Anthropic Claude, OpenAI GPT, Fernet-encrypted at rest), Analysis Templates, a REST API, webhooks, an MCP server for AI agents, and an embeddable pedigree viewer. It is designed to produce a clinical artefact — a report, an annotated pedigree, a risk number — not a research statistic.

The shape difference is the heart of the matter. QuickPed is a focused research instrument. Evagene is a clinical platform. Both are browser-based; both draw pedigrees; but they aim at very different outputs.

Feature-by-feature comparison

The matrix below compares publicly advertised capabilities. A tick means the feature is publicly documented; a dash means it is not publicly listed. Where QuickPed is stronger, the tick is on the QuickPed side; where Evagene is stronger, the tick is on the Evagene side. This is not a scoring contest — the two products overlap only partially.

Matrix compiled from publicly available product pages, the QuickPed paper (Vigeland, BMC Bioinformatics 2022;23:220), and the QuickPed manual as of April 2026. A dash does not imply absence — it indicates the capability is not publicly advertised.

What QuickPed does that Evagene does not try to do

It is worth being blunt: there is a set of things QuickPed does better than Evagene, and better than almost any other tool at any price point. Jacquard's nine condensed identity coefficients, X-chromosomal kinship variants, and a mathematically rigorous pairwise relationship description are capabilities rooted in decades of statistical genetics and the pedsuite package ecosystem. The relatedness triangle — plotting pairs of individuals in coefficient space — is the kind of visualisation that matters if your day job is forensic kinship analysis, population inbreeding surveys, or teaching a class on quantitative genetics. Building those capabilities competently requires either the pedsuite packages or a comparable re-implementation, and the pedsuite path is the sensible one: Magnus Vigeland and collaborators have done that work and published it under GPL3.

Evagene does not attempt to re-implement these tools. Evagene performs consanguinity detection with Wright's inbreeding coefficient, which is useful in clinical settings for flagging consanguineous unions where recessive disease risk is elevated, but it is not a substitute for QuickPed's full relatedness toolkit. If you need that toolkit, use QuickPed — the fact that it is free and free-software is a gift to the field.

What Evagene does that QuickPed does not try to do

The reverse asymmetry is also worth stating plainly. Evagene is built to produce clinical outputs: a named, ICD-10/OMIM-annotated family history; a BRCAPRO risk number that a clinician can discuss with a patient; a Lynch syndrome Amsterdam II eligibility flag; a drafted clinical interpretation paragraph an AI has generated from the pedigree for the clinician to edit and sign. It ships with a 200+ disease catalogue, four report types, PNG/SVG/PDF exports, and a platform layer that puts the pedigree into other clinical systems via REST, webhooks, MCP, or an embeddable viewer.

QuickPed does not aim at any of this and does not claim to. Its design centre is relatedness mathematics, not clinical workflow. That is a feature, not a gap — focused tools tend to be better within their scope, and QuickPed is a good example. But if you are running a clinical genetics service and need disease annotation, risk models, and auditable reports, QuickPed on its own will not do the job.

Using QuickPed and Evagene together

The most productive framing is cooperative. A realistic workflow might look like this. A clinical genetics service sees a consanguineous family with a suspected autosomal recessive condition. The counsellor builds the pedigree in Evagene during consultation (fast, clinical notation, disease annotation). For the relatedness detail — the precise kinship coefficient between the parents, the Jacquard coefficients across relevant pairs, or X-linked coefficient variants — the counsellor exports the structural pedigree, converts to PED format (straightforward with pedsuite helpers), and uploads to QuickPed for authoritative coefficient computation and the relatedness triangle plot. The numbers and the R code are pasted back into the Evagene case notes; the clinical report is generated in Evagene.

A research workflow might run the opposite direction. A research group builds a set of pedigrees in QuickPed during a population study (PED format, reproducible R code). For the ones that cross into clinical follow-up — families being invited into a genetic testing protocol, for example — the PED files are converted to GEDCOM and imported into Evagene, where disease annotation, testing status, and follow-up notes are added. The two tools do not fight each other; they sit at different stations in the same pipeline.

The PED and GEDCOM formats are the bridge. See our guide to GEDCOM pedigree software for why this matters and which tools handle what.

When to choose QuickPed

• Your primary question is mathematical: kinship, inbreeding, identity coefficients, X-linked variants, IBD triangles.
• You are working in forensic genetics, population genetics, ecology, or animal breeding.
• You want reproducible R code alongside your analysis.
• You are teaching statistical genetics and want a browser tool your students can use without installing R.
• You have a complex or unusual pedigree (cross-generational, deep consanguinity, historic royalty) and want a tool whose algorithms have been stress-tested on such cases.
• Your budget is zero and licensing overhead is unwelcome.

When to choose Evagene

• You run a clinical genetics service, cancer genetics clinic, or reproductive genetics service and need disease-annotated pedigrees.
• You need BRCAPRO, MMRpro, PancPRO, or Mendelian inheritance risk calculations as part of a clinical workflow.
• You want AI-assisted clinical report drafting using your own LLM keys.
• You need programmatic pedigree access via REST API, webhooks, MCP, or an embeddable viewer for patient portals and EHR integration.
• You need to move data between QuickPed/pedsuite research pipelines and a clinical system — Evagene's GEDCOM and JSON import/export make that practical.
• You need clinical reports (narrative, PDF) rather than coefficient tables.

Migration path between QuickPed and Evagene

The practical route is PED → GEDCOM → Evagene. QuickPed exports PED files (the de facto format of statistical genetics); Evagene imports GEDCOM 5.5.1 (the de facto format of genealogical and clinical pedigree exchange). The pedsuite R packages include utilities for converting between PED and other tabular formats; a short R or Python script can produce a GEDCOM from a PED file without much effort. Note the semantic gaps: PED files do not encode twin zygosity, carrier status, or deceased status, so those fields will need to be re-entered in Evagene after import. Disease annotations are likewise not part of the PED file; they are added in Evagene from the clinical notes.

Going the other way — Evagene to QuickPed — is simpler. Evagene exports pedigrees as GEDCOM 5.5.1 and as JSON; converting GEDCOM to PED for QuickPed consumption is a short R step using pedsuite's importers. The structural pedigree (individuals, parents, sex, affected status) transfers cleanly. Clinical annotations (diseases, risk models, AI interpretations) are dropped because QuickPed neither consumes nor needs them.

A note on respect

We want to say this explicitly. The QuickPed team have produced a genuinely first-rate open-source academic tool, published it properly, licensed it under GPL3, and maintained it as a public resource. That is the kind of work that moves the field. Writing a "competitor" comparison page that implies QuickPed is in any way second-rate would be both wrong and unfair. Evagene is a different kind of product with a different goal. Where the tools overlap, QuickPed is frequently the right answer; where they do not, Evagene is addressing clinical needs that QuickPed never set out to address. We recommend both in their respective domains.

Frequently asked questions

Related comparisons and reading

• Phenotips vs Evagene
• Progeny vs Evagene
• Pedigree drawing software: a field guide
• Clinical genetics pedigree tools
• GEDCOM pedigree software
• Mendelian inheritance calculator