A Free Vector NTI Alternative, and What to Do With the Export
Vector NTI has not been sold since 31 December 2019, and every licence and support contract stopped on 31 December 2020. Thermo Fisher's own FAQ is blunt about what that means: after that date there are no replacement keys, no reinstallation requests and no downloads. A copy that still runs somewhere in your lab is one machine rebuild away from being gone.
That leaves two problems, not one — getting your molecules out of Vector NTI's own database, and having somewhere to open them. This page is only the answer to the second, and it says so in the fourth row of the table: nothing here reads .ma4 archives. Thermo Fisher's Vector NTI Data Export Tool writes GenBank, and GenBank is the format SeqStudio and the rest of this site read best.
SeqBench vs Vector NTI
| Aspect | SeqBench | Vector NTI |
|---|---|---|
| Access model | Web app — no account, no licence key, nothing to install | Windows desktop install, activated with a licence key |
| Availability today | Live and maintained | Withdrawn. No sales since 31 December 2019; every licence and support contract stopped on 31 December 2020, after which Thermo Fisher issues no replacement keys, no reinstallations and no downloads |
| Price | Free | Was a paid licence; no longer sold at any price |
| Its own database files (.ma4, .pa4, .oar) | No — nothing here reads Vector NTI's native archives. Run Thermo Fisher's own Vector NTI Data Export Tool first; it writes GenBank, and GenBank is what this site reads best | Its own format, readable only by the software that is gone |
| GenBank records | Yes — the LOCUS line, DEFINITION, the whole FEATURES table including complement(...) and join(...) locations with their qualifiers, and the ORIGIN sequence | Yes — GenBank import and export |
| A multi-record GenBank file | Yes, and it says so: the viewer parses the first record and reports how many the file holds and which one it read, while the format converter turns every record in the file into FASTA, TSV or a rewritten GenBank in one pass | This is exactly what the Data Export Tool writes — one multi-record file per subfolder, plus a CSV of parent/child positions |
| SnapGene .dna files | Yes, both directions — read a colleague's .dna and write one back out | No — SnapGene reads Vector NTI's files, not the other way round |
| Editing a construct, with features that follow the edit | Yes — insert, delete or overtype bases and every feature's coordinates are recomputed against that edit, including a feature that wraps the circular origin. An edit that would half-delete a feature is held until you choose trim or delete, rather than applied silently | Yes — this was the core of the molecule editor |
| Restriction analysis and a gel | Yes — 566 enzymes, sites that span a circular origin included, single and double digests, and a drawn virtual gel | Yes, with its own enzyme database |
| Assembling Sanger reads (ContigExpress) | Yes, free — orientation worked out from the overlaps, ends trimmed by quality, and every position the reads disagree on listed. This is work you will have to redo: the export tool does not carry Contig projects | Yes, via the bundled ContigExpress module |
| Multiple alignment (AlignX) | Yes — a center-star alignment with a consensus and per-column conservation. It is not a progressive aligner: for a large or divergent family, MUSCLE or MAFFT is the better tool and this is not pretending otherwise | Yes, via the bundled AlignX module |
| Protein analysis (BioAnnotator) | Yes — molecular weight, pI with the full titration curve, extinction coefficient, GRAVY, aliphatic and instability indices, plus a windowed hydropathy profile | Yes, via the bundled BioAnnotator module |
| Primer design and oligo checks | Yes — primers from a template, nearest-neighbour Tm that responds to salt and Mg2+, hairpins, self-dimers and cross-dimers | Yes |
| A vector database to start from | Yes — 308 publicly deposited cloning and expression vectors, each with its accession, topology, full feature table and sequence | Yes — it shipped with a local vector database |
| A shared, multi-user molecule database | No. Saved work lives in your own browser, not on a server other people can reach: there is no team workspace, no permissions model and no shared registry | Yes — Vector NTI WorkGroup was exactly that |
| Working with no network at all | Partly. 26 of the tools run entirely in the browser and keep working offline; assembly, alignment, primer design and deep annotation call the server | Yes — a desktop program, offline by design |
| Where your file goes | GenBank and .dna files are parsed in your browser — both parsers are among the 26 that send nothing anywhere. Server-side tools receive the sequence for in-memory analysis; it is not logged or stored | On your own PC |
| API and AI-agent access | Yes — every tool behind a JSON REST endpoint and an MCP server | No public API |
Comparison is simplified and provided in good faith; the discontinuation dates and the export tool's behaviour are taken from Thermo Fisher's own product page and published FAQ. Vector NTI, ContigExpress, AlignX and BioAnnotator are or were products of Thermo Fisher Scientific and are not affiliated with SeqBench.
Where SeqBench is the better fit
- You have exported GenBank files and nothing left that opens them properly
- The export is one enormous multi-record file and you want every molecule out of it
- Your contigs and alignments have to be re-run, because the export did not carry them
- You are on a Mac or Linux, or on a machine you cannot install software on
- You want the same parsers from a script or an AI agent
Where Vector NTI still wins
- Reading its own .ma4, .pa4 and .oar archives — nothing here does
- A shared multi-user molecule database with permissions (WorkGroup)
- Working with no network at all
- The cloning and gene-synthesis project structure, which nothing exports
- If it still runs on your machine and you never rebuild it, it still works
What the export tool actually hands you
Worth knowing before you start, because two of these surprise people. The Data Export Tool converts a whole Vector NTI database to GenBank, GenPept, REBASE and CSV, keeping your subfolder structure as folders. Within each folder it writes multi-record GenBank rather than one file per molecule, alongside a CSV recording where each child sequence sits in its parent. Most browser tools will read the first record of a file like that and say nothing about the rest; the GenBank Viewer tells you how many records it found and which one you are looking at, and the format converter converts all of them in one pass.
The other surprise is what does not travel at all. Thermo Fisher's FAQ lists Contig projects, Alignment projects, Cloning projects and Gene Synthesis projects as unsupported by the export tool: the fragments come out as individual molecules, and which read went into which contig, and the parameters you ran, do not. Those have to be re-run — which is free here, with Sanger assembly for the contigs and multiple alignment for the families.
If what you actually have is a colleague's SnapGene file rather than a Vector NTI database, the longer writeup is in how to open a .dna file without SnapGene, which covers the Vector NTI and Serial Cloner cases too.
Where to start
Type or paste a sequence and edit it directly — every feature remaps live as you insert, delete, or replace bases, with undo/redo and GenBank import/export.
Paste a GenBank record and see an annotated circular or linear map with a feature table.
308 publicly deposited vectors with their full GenBank feature tables, and 617 parts harvested from them.
Frequently asked questions
Is Vector NTI really discontinued?
Yes, and Thermo Fisher says so on its own product page. Vector NTI Advance, Express and Express Designer were all withdrawn together: the last day licences could be bought was 31 December 2019, and all support ended on 31 December 2020. Thermo Fisher's published FAQ goes further than most people realise — after that date there are no replacement keys, no reinstallation requests and no free downloads, and every existing licence and support contract stopped. An installation that still runs is one machine rebuild away from being gone.
How do I get my molecules out of a .ma4 archive?
With Thermo Fisher's own Vector NTI Data Export Tool, which is still hosted for Windows and Mac and exports a whole database to GenBank, GenPept, REBASE and CSV. SeqBench does not read .ma4, .pa4 or .oar archives and is not going to pretend otherwise — no free browser tool reads them. Export first, then open the GenBank files here. SnapGene's own migration page claims it opens the native archives directly, which is the other route if the export tool will not run for you.
The export gave me one huge GenBank file. Now what?
That is normal: the Data Export Tool writes multi-record GenBank, one file per subfolder, with a CSV alongside it recording parent/child positions. Paste it into the GenBank Viewer and it parses the first record and tells you how many the file holds and which one it read, so you are never silently looking at one molecule out of forty. To get all of them, use the Sequence Format Converter, which converts every record in the file in one pass — to FASTA, to TSV, or back out as GenBank.
What happened to my ContigExpress and AlignX projects?
They did not survive the export, and this catches people out. Thermo Fisher's FAQ is explicit that Contig projects, Alignment projects and Cloning projects are not exported at all: the fragments come out as individual molecules, and the project settings — which reads went into which contig, the parameters you ran — are left behind. So those have to be re-run somewhere. The Sanger Trace Viewer assembles reads into a contig for free, and the Multiple Sequence Alignment tool realigns a family, both from the sequences the export did give you.
Is there a free replacement for the Vector NTI molecule editor itself?
SeqStudio is the closest thing here: a real editable sequence, not a viewer. Type into it and every annotated feature's coordinates are recomputed against that edit, including features that wrap a circular plasmid's origin, with undo/redo, live restriction digests and GenBank and SnapGene .dna import and export. Thermo Fisher's own FAQ names UGENE, Geneious, Benchling and SnapGene as software to check an export against; all four are either a desktop install or an account, which is the difference this one is trying to make.
What does Vector NTI do that this does not?
Three things, and they are in the table rather than buried. It reads its own native archives, which nothing here does. Vector NTI WorkGroup was a shared multi-user molecule database with permissions, and there is no equivalent here — saved work stays in your own browser. And it was a desktop program, so it worked with no network at all, whereas only 26 of the tools here run fully in the browser and the rest call a server.
Is my sequence uploaded anywhere?
GenBank and SnapGene .dna files are parsed in your browser: both of those parsers are among the 26 tools that run locally and send nothing. Tools that do run on the server — assembly, alignment, primer design, deep annotation — receive the sequence, analyse it in memory and return the answer; the input is not logged or stored.