Talindrew vs ApE: an ApE plasmid editor alternative in the browser
ApE is a free desktop plasmid editor by M. Wayne Davis that has served molecular biologists for two decades, and it does more than it usually gets credit for: annotation against a feature library, in silico PCR, Gibson, Golden Gate and restriction-ligation, primer design, and alignment to Sanger reads. Talindrew takes that same free spirit into the browser and goes considerably further: guided wizards with worked examples, four more cloning strategies, gel simulation, multiple sequence alignment, CRISPR guide design, a full lab notebook, protein structure prediction and an AI assistant.
Why choose Talindrew
Choose Talindrew if you want the guided version of the work ApE makes you drive yourself, and everything that sits either side of it. Six cloning wizards each ship a Load demo button, so you can walk a real Gibson or Golden Gate reaction end to end before touching your own sequences, and Gateway, TOPO/TA, In-Fusion and HiFi are there too. A cloning workspace ported from OpenCloning keeps a whole multi-step build as one graph and one portable strategy file. You also get an agarose gel simulator, multiple sequence alignment of up to 200 sequences, CRISPR guide design, methylation-aware digests over eleven REBASE enzyme sets, an electronic lab notebook, ESMFold structure prediction, a drug discovery pipeline and an assistant that reads your construct, with your work available on any machine you sign in from, and nothing to install.
Where ApE fits
ApE remains a lovely, fast desktop editor, and it is free: if all you want is a local window to look at a plasmid in, it has served people well for twenty years.
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Talindrew vs ApE, feature by feature
| Feature | Talindrew | ApE |
|---|---|---|
| Access | ||
| Free | Yes | Yes |
| Browser-native (no install) | Yes | No |
| Work follows you to any machine you sign in from | Yes | No |
| Runs offline, with no accountApE is a local desktop application: it opens a plasmid with no network and no sign-in. Talindrew runs in the browser and needs an account for the workbench, though the biomath calculators need neither. | No | Yes |
| Cloning | ||
| Guided wizards with a worked exampleApE simulates the reactions; you drive the design. Talindrew's six wizards walk the steps and each ships a Load demo button. | Yes | No |
| Reads and writes OpenCloning cloning-strategy filesTalindrew's cloning workspace is a port of OpenCloning and saves its cloning-strategy JSON, so the whole build history of a construct travels as one file. | Yes | No |
| Node-graph workspace with sixteen operationsApE simulates a reaction at a time. Talindrew keeps the whole strategy as a graph: digest, PCR, oligonucleotide hybridisation, polymerase extension, reverse complement, annotation, the Gibson family, restriction and ligation, ligation, homologous recombination, CRISPR-HDR, Gateway, Cre/Lox and recombinases. | Yes | No |
| Kit templates and a syntax-driven Golden Gate assemblerMoClo YTK and the rest of the OpenCloning kit templates, with a category chain that assembles every valid combination at once. | Yes | No |
| Gateway, TOPO/TA, In-Fusion and HiFi | Yes | No |
| Simulates Gibson, Golden Gate and restriction-ligation | Yes | Yes |
| Analysis | ||
| Agarose gel simulation | Yes | No |
| Multiple sequence alignmentApE aligns Sanger reads against a reference. Talindrew adds a multiple sequence alignment of up to 200 DNA or protein sequences, with consensus, conservation, an identity matrix and a tree. | Yes | No |
| CRISPR guide design | Yes | No |
| Codon optimisation | Yes | No |
| Restriction digest | Yes | Yes |
| Methylation-aware digest | Yes | Yes |
| PCR primer designApE does virtual PCR and primer design. Talindrew ranks primer pairs on Tm, GC clamp, hairpins, dimers, product size and binding-site count, and builds 5′ overhangs for restriction sites, tags and Gibson arms. | Yes | Yes |
| Sanger read alignment | Yes | Yes |
| Lab operations | ||
| Electronic lab notebook | Yes | No |
| Structure | ||
| Protein structure prediction | ESMFold, on Pro | No |
| Drug discovery pipeline | Yes | No |
| AI | ||
| Sequence-aware AI assistant | Yes | No |
| Editing | ||
| Zoomable, modern UI | Yes | No |
| Linear sequence editor | Yes | Yes |
| Circular plasmid map | Yes | Yes |
Talindrew vs ApE: common questions
Yes. ApE (A Plasmid Editor) by M. Wayne Davis at the University of Utah is still actively updated, runs on macOS, Windows and Linux, and remains free. A paper describing it was published in Frontiers in Bioinformatics in 2022.
For the guided version of work ApE makes you drive yourself, and for everything either side of it. ApE simulates PCR, Gibson, Golden Gate and restriction-ligation and designs primers. Talindrew wraps six strategies in wizards that each ship a worked example, adds Gateway, TOPO/TA, In-Fusion and HiFi, and then adds gel simulation, multiple sequence alignment, CRISPR guide design, codon optimisation, a full lab notebook, protein structure prediction, a drug discovery pipeline and an AI assistant: in a browser, with your work on every machine you sign in from.
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