Frequently asked questions

Digital Seed is a cloud-based plant genomics platform that turns marker and phenotype data into breeding decisions. It bundles GWAS, genomic selection, population structure, multi-environment trial analysis, selection indices, gene annotation and environmental intelligence into a single web workflow — no server setup, no scripting required.

Public breeding programs, seed companies, agri-biotech startups, and plant science researchers. If you have SNP genotypes and phenotype records for a crop, you can use Digital Seed.

No. Digital Seed runs entirely in your browser. All computation happens on our managed backend.

Species-agnostic — any diploid or polyploid crop with SNP data works. We ship curated reference panels and gene models for major crops (wheat, maize, rice, soybean, tomato, cotton and more); see the Crops page for the full list.

VCF (v4.1+), PLINK (.bed/.bim/.fam), HapMap and tab-separated numeric matrices. Files can be gzipped. Multi-sample VCFs up to several GB are supported.

CSV or TSV with one row per genotype/environment. The first column is the accession ID; subsequent columns are trait values or factor levels. Missing values as NA or empty are handled automatically.

By default, all uploaded datasets, analyses and results are automatically deleted 7 days after upload. Export any results you want to keep. Paid tiers can extend retention.

No. Your data is private to your account and protected by row-level security. We do not train models on your data and never share it with third parties. See the Privacy Policy for details.

Mixed-linear model (MLM), compressed MLM, FarmCPU and BLINK, with optional kinship and principal-component covariates. Multiple-testing correction uses Bonferroni or Benjamini–Hochberg FDR.

GBLUP by default, with optional Bayesian ridge, BayesA, BayesB and RKHS models. Cross-validation splits, prediction accuracy and reliability are reported for every run.

Yes. Every analysis stores its exact inputs, parameters, software versions and random seed. Any run can be rerun with one click, and results can be exported as BibTeX or RIS for citation.

A GWAS on 500 accessions × 50k SNPs finishes in 1–3 minutes. Genomic selection with 5-fold cross-validation on similar data takes 3–8 minutes. Progress is streamed live.

Yes. The free tier includes a monthly quota of analyses, limited storage and a cap on concurrent runs. See the Pricing page for current limits.

New runs are blocked until the next monthly reset or until you upgrade. Existing results remain accessible. Quota usage is visible in your dashboard at any time.

Yes. Cancellation is self-service from your account settings and takes effect at the end of the current billing period.

Ten production-accurate quantitative-genetics analyses are embedded directly into the module they belong to — no separate lab. ADE-GBLUP (A+D+A×A variance) lives in /app/gblup. Finlay–Wilkinson G×E stability lives in /app/met. Smith–Hazel multi-trait selection index lives in /app/multi-trait-gs. Coloc-ABF (PP0–PP4) lives in /app/finemap. Cox-PH survival GWAS lives in /app/gwas-ext. Pairwise G×G epistasis with BH q-values lives in /app/gwas-plus. LocusZoom-style regional plots live in /app/gwas. IM/CIM QTL with Churchill–Doerge permutation thresholds lives in /app/deep-genomics. Stratified HWE (Wigginton exact + Fisher-combined) and PLINK-style sex check live in /app/hwe-maf. Sliding-window π with moving-block bootstrap CIs lives in /app/diversity.

They are unlocked on the Lab, Institute and Enterprise plans. Sprout, Seedling and Breeder users see a locked upgrade card on each host page with a direct link to /pricing.

ADE-GBLUP and epistasis take a numeric SNP dosage matrix (0/1/2) plus a phenotype vector. Finlay–Wilkinson takes a genotype × environment trait matrix. Smith–Hazel takes phenotypic (P) and genotypic (G) covariance matrices plus economic weights. Coloc-ABF takes β/SE vectors for two traits over the same SNPs. Cox-PH GWAS takes a covariate/dosage matrix with time-to-event and event indicator. QTL mapping takes a −1/0/1 genotype matrix plus a linkage map (chrom, cM). Stratified HWE takes per-stratum AA/Aa/aa counts. Sex-check takes X-chromosome dosages and reported sex. π-windows takes per-site allele frequencies with sample size and window/step in base pairs.

Lab: up to 50,000 samples, 10M markers, 20 traits per job, 2,000 runs/mo. Institute: uncapped for practical usage with fair-use. Enterprise: uncapped with dedicated compute priority. Every host page shows your plan's limits above the runner card and blocks the run with an upgrade CTA when exceeded.

Open the host module page (e.g. /app/gblup for ADE-GBLUP, /app/met for Finlay–Wilkinson, /app/diversity for π-windows). Each host has a one-click 'Run demo' card with a deterministic input to validate the pipeline end-to-end. Then wire your own dataset via the standard Digital Seed uploaders on the same page. If your plan doesn't include the analysis, the card shows an upgrade link to /pricing.

Passwords are hashed with bcrypt and checked against the HaveIBeenPwned leaked-password database at signup and reset. We support email OTP and OAuth sign-in.

Google OAuth is enabled by default. SAML SSO for institutions is available on the enterprise tier.

On managed cloud infrastructure with encryption in transit (TLS 1.3) and at rest (AES-256). Backups are geographically redundant.