Every tool, grouped by what it does.

Constrained combinatorial generation over real, controllable parameters — regulatory context, codon target, guide choice. Every candidate is scored by the predictors and run through the validators and biosecurity gate before it is ever proposed. A blocked candidate is dropped, not ranked.

One free-text instruction, decomposed into an ordered tool plan and chained end to end — e.g. express this, then predict its yield. The deterministic intent router classifies modality, method and delivery first, so the plan is auditable.

A plain-English explanation of any design where every claim is backed by an engine output or a citation. The LLM is hard-constrained to restate only the facts it was given — it cannot introduce an ungrounded number.

Knockout / knock-in across Cas9 (NGG), Cas12a (TTTV), λ-Red, integrase, base & prime editing. Host-universal delivery, a CFD-style genome off-target screen, an HDR donor with re-cut prevention, and verification primers.

HGVS-lite edits like S65T, F64L, K27del — frame-preserving, with primer design and a re-check of the resulting construct. The exact deterministic move a bench scientist would make, automated.

Gibson, Golden Gate, MoClo and BioBrick RFC[10], plus a modern suite — In-Fusion, Gateway BP/LR, TOPO, restriction-ligation. Both-strand domestication scan so no method-breaking site slips through.

N/C-terminal tags, linkers, NLS/NES localization signals, secretion leaders and protease sites — composed and validated as one construct, with the junctions checked.

NNK/NNS site-saturation and combinatorial promoter × RBS libraries, with the diversity math worked out — theoretical size, codon coverage and the screening burden you're signing up for.

Operons, pathways and toggle-switch circuits — multiple coding sequences with their own regulatory parts, assembled and balanced into a single plannable construct.

Live, continuous QA: frameshift, premature stop, cryptic ORF, illegal restriction site, low-complexity/repeats, splice site, polyA signal — returned as structured findings with severity, so a UI can underline problems as you type, exactly like a code linter.

Needleman–Wunsch (global) and Smith–Waterman (local) alignment, plus Sanger trace reading — confirm an edit landed and read the chromatogram without leaving the workspace.

Tm, hairpin, self- and cross-dimer, and specificity for any primer set — flagged before you order, not after a failed reaction.

A fast offline foldability heuristic runs in-loop on every Express design; a deep AlphaFold / ESMFold prediction with per-residue pLDDT confidence bands is available on demand.

ORF and feature analysis plus render-ready map tracks for a SnapGene-style plasmid view — GC ring, bp ruler, directional feature arrows, single-cutter enzyme ticks — drawn client-side with no libraries.

A precise design diff between two constructs or two versions — what changed, where, and why — feeding the version-control timeline and the side-by-side comparison report.

A CFD-style specificity prediction for a guide against the host genome — value plus confidence interval, with the evidence sites it scored.

Cutting efficiency for a chosen guide, scored with the same uncertainty contract — so you rank guides on evidence, not vibes.

Reference-model soluble yield in mg/L with a transparent factor breakdown — codon adaptation, GC, host, regulatory strength — so you see why, not just a number.

Multi-objective ranking with a true Pareto front — surface the non-dominated trade-offs (yield vs. specificity vs. cost) instead of collapsing them into one fragile score.

An in-house bench-results store with CSV/JSON ingest, a predicted-vs-observed reconciliation, and a closed-form least-squares calibration tracker (with R²) — so the predictors get sharper as your data grows.

UCB / EI / uncertainty acquisition with a diversity penalty — it picks the batch that teaches you the most per dollar, not just the highest-mean candidates.

Git-like repos for constructs — branch, commit, log, diff, blame, with per-base attribution. Treat a plasmid like a codebase, with a real history you can audit.

The container that holds runs, repos, campaigns, sessions, data and files together — with an activity log and inline named sequences. A tabbed workspace: Overview · Repos · Campaigns · Chats · Data · Files · History.

A deterministic NL edit-and-re-check: "swap the promoter for EF1α and re-optimize" applies the edit, then re-runs the linter, analysis, foldability and yield automatically.

One-way, opt-in export to your ELN. Quill's GenBank output opens directly in the sequence tools you already use — design-intelligence in, system-of-record out. It never ingests from or depends on an ELN.