Trying to implement Needleman-Wunsche algorithm for biological sequences comparison. In some circumstances there exist multiple optimal edit paths.
What is the common practice in bio-seq-compare tools handling this? Any priority/preferences among substitute/insert/deletion?
If I want to keep multiple edit paths in memory, any data structure is recommended? Or generally, how to store paths with branches and merges?
Any comments appreciated.
As a lot of similar algorithms, Needleman-Wunsche one is just a task of finding the shortest way into a graph (square grid in this case). So I would use A* for defining a sequence & store the possible paths as a dictionary with nodes passes.