Docs

Learn deoxy, step by step.

Guides for every part of the workspace, from your first import to full cloning workflows. New here? Start with the Quickstart.

Getting started

Quickstart: your first document5 minA tour of the workspace, then a full path from import to cloning: import a plasmid > read its annotations > make your first cloning product.Read guide
Tour of the interfaceComing soonThe nav rail, sidebar, editor, and bottom panel in depth.

Importing

Importing sequences8 minEvery way to get data into deoxy (local files, accessions, and gene symbols), the supported formats, and how deoxy automatically decides whether a file becomes a sequence, a genome, an alignment, or a group.Read guide

Documents & organization

Documents, labels & searchComing soonDoc types, organizing with labels instead of folders, search, and sharing links.
Version history & sharingComing soonRestore earlier versions and generate read-only share links.

The editor & its dials

The editor & its dialsComing soonEvery Layers toggle, zoom, reading frame, complement, translation, palettes, circular and 3D views.

Annotations

Working with annotationsComing soonAdd features, import from CSV, and use the annotation prediction engine.

Alignments

Pairwise & multiple-sequence alignmentComing soonNeedleman-Wunsch, Smith-Waterman, translation, Clustal Omega, MUSCLE, MAFFT, and T-Coffee.

Reference maps

Mapping reads to a referenceComing soonMap documents or SRA runs, choose a mapper and sensitivity, and read coverage and variants.

Cloning workflows

Restriction sites & non-cuttersComing soonMap cut sites, filter by enzyme set and recognition length, and find non-cutters.
Restriction cloningComing soonCut a backbone and insert with shared sites.
Gibson & Golden Gate assemblyComing soonHomology-arm and Type IIS multi-part assembly with primer design.
Codon optimizationComing soonImprove expression for a target host with motif and homopolymer constraints.

Primers

Designing primersComing soonTarget a region, set constraints, and pick pairs with Primer3.
Validating & importing primersComing soonCheck binding against a reference or SRA reads, and import existing primers.

Trees & phylogeny

Building phylogenetic treesComing soonFastTree and neighbor-joining trees, and distance matrices.

deoxy is in active early access, and these guides ship alongside the product. Missing something you need? Founding users have a direct line to the developer.

Join the waitlist See the changelog