Feature glossary

Genome-wide association: baseline (GWAS), advanced with covariates & annotation (GWAS+), and case–control binary phenotypes (GWAS-CC).

Predict breeding values from genotypes. GS uses rrBLUP; GS+ adds kernel/Bayesian priors; GBLUP uses the genomic relationship matrix.

Best linear unbiased estimates/predictions for field phenotypes plus realized kinship (GRM) computation.

Impute missing genotypes against a reference panel and annotate variants with gene, consequence, and functional impact.

Cross-genome synteny, orthologs, and core/accessory (PAV) analysis across a pangenome.

Applied ML pipelines for yield prediction, stress tolerance, and pedigree/genotype-based breeding decisions.

Multi-environment trials with G×E, population genetics (Fst, LD, diversity), ancestry/PCA structure, and field trial design.

Analysis of molecular variance, Mantel isolation-by-distance tests with permutation p-values, and LD-based effective population size (Ne) estimation.

Multi-locus association mapping: FarmCPU iterative fixed/random and MLMM stepwise selection with extended BIC.

Bayesian genomic prediction via Gibbs sampling: BayesA, BayesB (with π), and Bayesian LASSO with cross-validation.

Nucleotide diversity π, Watterson's θ, Tajima's D, and unfolded Fay–Wu H / Fu–Li D & F when ancestral alleles are provided.

Fine-mapping (SuSiE), selection signatures, quantitative-genetics workbench, randomized trial layouts, and polygenic risk/merit scores.

Query external biological databases directly from the app: Ensembl gene lookups, NCBI records, KEGG pathways.

Ten advanced analyses embedded directly into their host modules (gBLUP, MET, Multi-trait GS, Fine-map, GWAS+/ext, Deep Genomics, HWE/MAF, Diversity): additive+dominance+epistasis GBLUP variance, Finlay–Wilkinson G×E stability, Smith–Hazel selection index, Giambartolomei ABF colocalisation (PP0–PP4), Efron-equivalent Cox-PH survival GWAS, pairwise A×A epistasis with BH q-values, LocusZoom-style regional plots, IM/CIM QTL with Churchill–Doerge permutation thresholds, Wigginton exact + Fisher-combined stratified HWE with PLINK-style sex check, and sliding-window nucleotide diversity π with moving-block bootstrap CIs.

Download raw tables (SNP hits, EBVs, QC stats) as CSV files.

One-click styled PDF reports with plots and result tables, ready to share.

Full result bundle: report.pdf, results.json, metadata.csv, dataset/pipeline IDs and SHA-256 integrity hashes for every file.

Every run is saved with its parameters and inputs; re-run any experiment with a single click.

Heavy runs execute in a background queue; progress streams to the UI with retries on transient failures.

Signed export packages that capture inputs, parameters, versions, and outputs so any collaborator can reproduce the run.

Team-shared collections of datasets and results plus a collaborative lab notebook.

Programmatic REST access, outbound webhooks on job events, typed SDK, and bulk job submission.

SAML single sign-on with fine-grained role-based access control.

Number of standalone PDF report downloads permitted per month.

Number of full ZIP result bundles (PDF + JSON + metadata + hashes) permitted per month.

How many export packages can be built in parallel by a single user.

How many heavy analyses can run at once for your workspace.

How long completed export artifacts remain downloadable.

Queue priority tier — higher tiers preempt lower-tier jobs during peak load.

Guaranteed first-response time for support tickets.

Immutable log of user and system actions with configurable retention.

Where the platform runs — shared multi-tenant cloud or your own private/on-prem environment.

Contractual monthly uptime guarantee.

Distinct workspaces isolating datasets, runs, and members.

Seats included in the plan.

Total data at rest across datasets and result bundles.

Number of analysis jobs you can launch each month.

Largest single file the uploader accepts (resumable on higher tiers).