Sequence alignment with one to many characters I'm trying to align a sequence of characters together, I found that sequence alignment algorithms which use dynamic programming like Needleman-Wunsch or Smith–Waterman only align one character with one character beside allowing character substitution, deletion or insertion.

For example, if I have a set of similarly sounding characters, like

monir, monier, muneer, munir, mounir, mouneer


The alignment algorithm will produce the following output

m u n i - r
| | | |   |
m o n e e r


Is there a way to adapt these algorithms (or an alternative algorithm) to consider aligning/substituting character with more than one character in order to output something like

m u n i  r
| | | |  |
m o n ee r


Please note that, I'm using the standard java implementation for these algorithms and I don't have a predefined list of similarly sounding characters, so I'm trying to aligning the similar words together in order to extract these alignments.
If I understood your problem correctly, a trie data structure may help you. The main challenge would be after the first mismatch, match the upcomming characters. I'm not sure how I would hack it, but it may not be that hard.

Hope it helps. Regards