tie-breaking in nwalign
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Now that nwalign exists within the MEX simplegapmex, I cannot see exactly how it is implemented and I'm not able to get it to agree with a MEX version of needleman-wunsch that I wrote (with some slightly different properties). I'd like the behavior to be exactly the same but they produce slightly different alignments. While the two versions produce identical dynamic programming matrices, simplegapmex always goes with different paths back through them, no matter what order of preference I give to moves up, left, or diagonal in cases of ties. so... how are ties being broken by simplegapmex when there are multiple equally scoring paths through the DP-matrix?
Lucio Cetto on 18 Oct 2011
Under ties, the simplegap algorithm favors first diagonal (matches/missmatches) then gap instertions in the first sequence and finally gap insertions in the second sequence.