Alignment of things other than DNA or Protein Sequences

Question

[murphytho1401]

This is a bit of a strange question, but I was wondering if anyone knew of any tools that would allow me to create an alignment (ideally a multiple sequence alignment but I can do multiple pairwise alignments too) of words instead of DNA or protein sequences?

As an example, let's say I had three lists:

I would love a tool to spit out something like this:

Sorry for the format, but I hope you get the idea. I'm hoping to avoid having to code the whole algorithm myself or do it manually. Thanks in advance for any ideas!

Answer 1

[Mensur Dlakic]

In principle, you can align anything to anything given some kind of a substitution matrix that tells the program how to score the alignments. Depending on how many unique words are in your dataset, you can still simplify it down to single letters (yellow->Y, red->R, etc). It also depends on whether you are looking for absolute identity or if some color can substitute for each other even when non-identical (say, orange and red or orange and yellow). Again, a substitution matrix would specify if any imperfect matches are permissible.