With just two sequences you can use Needleman-Wunsch. It’s a dynamic programming algorithm that provides an optimal alignment (good thing, although there may be more than one optimal alignment), but it doesn’t scale well (not good thing). I describe an XSLT 3.0 implementation in my 2020 XMLPrague paper at https://archive.xmlprague.cz/2020/files/xmlprague-2020-proceedings.pdf

Your question doesn’t clarify whether you’re looking for index numbers in the alignment (where a word in one input might be matched by a gap in the other) or in the inputs (where aligned words share a position in the alignment but may have different positions in the inputs). For either of those interpretations, though, a solution will begin by finding an alignment.

David J. Birnbaum

djbpitt@gmail.com

On Feb 11, 2026, at 9:41 PM, Graydon Saunders <graydonish@fastmail.com> wrote:

Hello!

If I have two (fairly long) sequences of text, ('The', 'words', 'are', 'sequence', 'members') and I want all the index numbers of matching pairs despite the sequences only mostly matching (so a word, or several words, can be missing from sequence A or sequence B), is there an established algorithm for doing this?

(If I search on "aligning sequences" I get bioinformatics about gene sequences; if I search on "aligning text" I get typography.)

Thanks!
Graydon