Interactive alignment demo with different algorithms
These JavaScript pages are specifically for teaching purposes.
They do not use affine gap penalties (they make no distinction between gap opening and gap elongation), and they are suitable for
short sequences only.
Thanks to Mostafa Mohmmed for releasing the code on github https://github.com/drdrsh/Needleman-Wunsch
and Chris Lockhart, https://lockhartlab.org/ for extending it.
Further modified by Peter Wad Sackett for use in course 22111 - Introduction to Bioinformatics at Technical University of Denmark.
Alignment tool
This tool is a reimplementation in JavaScript of the "Needle" and "Water" tools from the EMBOSS software (written in C).
It features:
- user-adjustable affine gap penalties,
- optional end gap penalties in Needleman-Wunsch,
- a choice of four BLOSUM matrices and three PAM matrices for protein alignment,
- an option to upload additional substitution matrices.
Thanks to Isaac Francis Chan for doing the main part of the vibe coding.