MUSCLE is one of the most widely used multiple sequence alignment program for protein and nucleotide sequences. It is written in C++ by Robert C. Edgar and its source code is available on GitHub.
I compiled MUSCLE to WebAssembly (WASM) using Emscripten to make it available as a zero-install fully client-side app. You can try it out below using my WASM shell.
You can start by running
muscle with no arguments to see the usage instructions. To execute MUSCLE on the example seqs.fa file that is already present in the file system, run
muscle -align seqs.fa -output seqs.afa.