comparing between two alignments

Question

[QAZ]

Dears,

When comparing between two alignments A, B for the same data set but different algorithm (e.g alignment A from ClustalW and alignment B from MUSCLE), suppose alignment A has less number of SNPs. Does less number of SNPs make alignment A better than alignment B? If yes please mention some papers talking about that.

Thank you in advance.

[M.O.L.S]

There should be research articles about clustalW and MUSCLE available in the same area where you found and downloaded the programs. If you are looking at alignments it will depend on the scoring function. I would say less amount of gaps makes alignment A better than alignment B.