Enumerating suboptimal alignments of multiple biological sequences efficiently

Tetsuo Shibuya and Hiroshi Imai
Proc. 2nd Pacific Symp. Biocomputing, Jan 1997, pp. 409–420
http://www-smi.stanford.edu/people/altman/psb97/shibuya.pdf

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Finding the $k$ shortest paths

Fano Experimental Web Server, D. Eppstein, School of Information & Computer Science, UC Irvine