Post

New set of thesis figures on pairwise alignment just dropped! - schematic and worked example for many algorithms - alignment modes

Ragnar {Groot Koerkamp}

@curiouscoding.nl

And some more: - edit graph - cubic DP (as N&W originally introduced it) + quadratic DP (as fixed by many others) - cost models

27/3/25, 4:30 pm0 reposts4 likes

Ragnar {Groot Koerkamp}

@curiouscoding.nl

27 Mar 2025

See them in action here :) Although I may have to split the large ones so they go part-by-part. curiouscoding.nl/posts/pairwi...

curiouscoding.nlA History of Pairwise AlignmentTable of Contents 1 A Brief History 1.1 A*PA 1.2 A*PA2 1.3 Overview 2 Problem Statement 3 Alignment types 4 Cost Models 4.1 Minimizing Cost versus Maximizing Score 5 The Classic DP Algorithms 6 Linear...

Ragnar {Groot Koerkamp}

@curiouscoding.nl

27 Mar 2025

Happy to get suggestions for improving them btw :)

Seth Stadick

@ducktapeprogrammer.bsky.social

27 Mar 2025

It's been very cool to watch the content on your site grow. I've been dabbling with some alignment adjacent things and your posts have been invaluable.

Seth Stadick

@ducktapeprogrammer.bsky.social

27 Mar 2025

Question on semi-global alignment - where did you find / come up with the names of "overlap", "extension", etc? I'd always thought of all of those as just variants of semi-global.

Seth Stadick

@ducktapeprogrammer.bsky.social

27 Mar 2025

My basis for what is semi-global is coming from only two sources though. This set of slides from @robp.bsky.social rob-p.github.io/CMSC423_S20/... And the source code for parasail.

rob-p.github.iorob-p.github.io