Sequence Aligner v1.1 (Windows app, with on-device AI)

A tunable DNA and protein sequence aligner as a native Windows app, now with on-device AI.

How to run

1. Download SequenceAlignerApp-win-x64.zip below.
2. Unzip it into a folder.
3. Run SequenceAlignerApp.exe.

Self-contained (no .NET install needed). The 3D and AI features use an internet connection for structure data.

New in v1.1

• AI protein analysis: a transformer language model (trained from scratch) scores how related two proteins are, predicts the family of a sequence, and finds similar proteins in a built-in database. Runs on the GPU or NPU (Windows ML).
• AI secondary-structure prediction (helix / sheet / coil), also on the GPU/NPU.
• Cytochrome c sample, plus everything from v1.0 (global/local/semi-global, banded whole-genome alignment, affine gaps, the 3D structure viewer, dot plot, and more).

Sequence Aligner v1.0 (Windows app)

A tunable DNA and protein sequence aligner as a native Windows app.

How to run

1. Download SequenceAlignerApp-win-x64.zip below.
2. Unzip it.
3. Run SequenceAlignerApp.exe.

It is self-contained, so you do not need to install .NET or anything else. The 3D viewer and the AI structure feature need an internet connection.

What it does

Global, local, and semi-global alignment; linear or affine gaps; DNA or protein (BLOSUM62 / PAM250); whole-genome alignment with a banded method; a colored alignment view with readouts; a 3D structure viewer; and an AI secondary-structure predictor that runs on the GPU or NPU.