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 pedigree management platform aimed at genetics teaching and research, with integrated BayesMendel cancer risk models, a curated disease catalogue, AI-assisted draft summaries for educational / research review, and a platform layer (REST API, webhooks, MCP, embeddable viewer). QuickPed and Evagene overlap more than they used to. As of June 2026 Evagene ships an educational / research relatedness and IBD suite — full pairwise kinship coefficients, per-individual inbreeding, Jacquard k0/k1/k2 identity, and gene-dropping relatedness simulation — so basic relatedness questions can now be answered inside Evagene too (gated, for education and research, never forensic). QuickPed still owns the capabilities Evagene does not replicate: X-chromosomal coefficient variants, the relatedness-triangle visualisation, the novel natural-language pairwise-relationship algorithm, reproducible R-code output, and a forensic / ecology / animal-breeding remit backed by a peer-reviewed publication. If your question is "what should the educational report on this family say, and how does the illustrative BRCAPRO number look?" Evagene is the right tool; if it is "give me the X-linked identity coefficients with reproducible R code for a forensic case," QuickPed is. 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 June 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 pedigree drawing, management, and modelling. Its emphasis is the clinical pedigree as a live working document: a gesture-drawing canvas for construction during consultation, standard NSGC/ISCN notation, a 230+ disease catalogue annotated with ICD-10 and OMIM codes, integrated BayesMendel cancer risk models (BRCAPRO, MMRpro, PancPRO), Mendelian inheritance calculators, AI-assisted draft summaries for educational / research review 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 June 2026. A dash does not imply absence — it indicates the capability is not publicly advertised.

Relatedness mathematics: where the two now overlap

This used to be the section where we said QuickPed simply does relatedness and Evagene does not. That is no longer accurate. As of June 2026 Evagene ships a relatedness and IBD suite of its own: full pairwise kinship coefficients, per-individual inbreeding, Jacquard k0/k1/k2 identity, and gene-dropping relatedness simulation. It is gated and framed for educational and research use — explicitly not a forensic tool — but for a service that wants kinship and identity numbers alongside its pedigree, the basic relatedness questions can now be answered inside Evagene rather than exported.

It is still worth being blunt about what QuickPed does that Evagene does not. X-chromosomal kinship variants, the relatedness-triangle visualisation (plotting pairs of individuals in coefficient space), and the mathematically rigorous, natural-language pairwise-relationship description are capabilities rooted in decades of statistical genetics and the pedsuite package ecosystem, and Evagene does not replicate them. Nor does Evagene emit reproducible R code, carry a peer-reviewed publication behind its algorithms, or aim at the forensic, ecological, and animal-breeding domains QuickPed serves. Those remain genuine QuickPed strengths: Magnus Vigeland and collaborators have done that work and published it under GPL3, and the fact that it is free and free-software is a gift to the field. Evagene continues to run consanguinity detection with Wright's inbreeding coefficient for clinical flagging of consanguineous unions; for the X-linked coefficients, the triangle plot, the relationship-description algorithm, or any forensic use, QuickPed is the right tool.

What Evagene does that QuickPed does not try to do

The reverse asymmetry is also worth stating plainly. Evagene is built around a structured, documented family history: an ICD-10/OMIM-annotated pedigree; an illustrative BRCAPRO output for teaching and research review; a Lynch syndrome Amsterdam II worked example showing how published criteria may be represented; an AI-assisted draft summary generated from the pedigree for an educator or researcher to review and edit. It ships with a 230+ disease catalogue, four report types, PNG/SVG/PDF exports, and a platform layer that puts the pedigree into other systems via REST, webhooks, MCP, or an embeddable viewer. Outputs are illustrative and for educational / research purposes, not clinical recommendations.

QuickPed does not aim at any of this and does not claim to. Its design centre is relatedness mathematics. That is a feature, not a gap — focused tools tend to be better within their scope, and QuickPed is a good example. Where Evagene differs most is its open agent surface: an MCP (Model Context Protocol) server exposing 27 tools so AI agents such as Claude Desktop and Claude Code can read and build pedigrees; an “Evagene Pedigree Builder” ChatGPT Custom GPT that turns a natural-language family-history description into a structured pedigree; and a Related Concepts educational correlation graph (1,100+ curated associations) linking diseases, genes, and findings as reference material — educational data, not risk analysis or diagnosis. QuickPed publishes neither an MCP server nor a Custom GPT for pedigree building; as of June 2026, none of the tools compared on this site does.

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) and reads off the pairwise kinship, per-individual inbreeding, and Jacquard k0/k1/k2 figures from Evagene's own educational relatedness suite. For the detail Evagene does not produce — X-linked coefficient variants, the relatedness-triangle plot, the natural-language pairwise-relationship description, or reproducible R code for a publication or forensic case — the counsellor exports the structural pedigree, converts to PED format (straightforward with pedsuite helpers), and uploads to QuickPed for authoritative computation. The numbers and the R code are pasted back into the Evagene case notes; the educational 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 and needs capabilities Evagene does not replicate: X-linked coefficient variants, IBD / relatedness triangles, or the natural-language pairwise-relationship description. (Basic pairwise kinship, inbreeding, and Jacquard k0/k1/k2 are now available in Evagene too, for educational and research use.)
• 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