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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 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.

vanilla
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  • I see no Java code in your question. Did you write any code? Does it work? If not, what error do you get? –  Apr 24 '15 at 12:33
  • You might want to try this website as well http://cs.stackexchange.com/ – panagdu Apr 24 '15 at 12:36
  • @Tichodroma I'm just using a java implementation of the standard algorithms like https://code.google.com/p/himmele/source/browse/trunk/Bioinformatics/SmithWaterman/src/SmithWaterman.java – vanilla Apr 24 '15 at 12:37
  • I am afraid SO is not the site to ask this kind of question. It is an algorithm question better asked in http://cs.stackexchange.com/ –  Apr 24 '15 at 12:40
  • Do you want to really align the sequences or your objective is to find if two words are equivalent considering those similarly sounding characters? – Juan Lopes Apr 24 '15 at 14:38
  • @JuanLopes actually, I need both. I need an algorithm that can align character with more than one character in a string. Also, I need to extract the possible characters that can be aligned together without affecting the score of alignment which I think that can be collected from a training dataset with similar sounding character. – vanilla Apr 24 '15 at 20:12
  • Do you have a list of all equivalences? – Juan Lopes Apr 24 '15 at 20:16

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