Hi, there I am new in statistics, forgive me if this question is too silly. I want to test if one alignment method is better over another one. To do this, I use a bunch of sequence pairs as benchmark and aligned them using these two method, respectively. By comparing the alignment with 3D structure superimposed alignment, I can get a score (s1 for method one and s0 for original method) for each alignment method on pairs I selected. What statistical test should I choose? I want to use a binomial test. but, It seems this test only takes two set of data, either s1>s0 or s1<s0. howver, in my case sometimes two methods have the same score, how to deal with the situation when s0 = s1? Or should I use paired t-test? regards John