The problem with the MSA question is that there is no objective measure of goodness. Most people compare them to a subjective 'gold standard', which is a manual

The problem with the MSA question is that there is no objective measure of goodness. Most people compare them to a subjective 'gold standard', which is a manual alignment. Black box comparisons are not progressive: the only non-subjective advances can come from incorporating the results of sequence evolution experiments into the algorithms, and then the algorithm needs to be trusted, for which it needs to be open to scrutiny. I agree about the genetic algorithm.