MSA ensemble

"Ensemble" is my jargon for a collection of alternative MSAs of the same sequences. One MSA in an ensemble is called a replicate .

With stratified ensembles and diversified ensembles , the same sequences appear in all alignments.

With stratified and diversified ensembles generated by align or super5 , all replicates have equal accuracy on benchmark tests , noting that the replicate generated with default parameters is no better than any other on average. Therefore,

(1) there is no preferred replicate, including a replicate generated with default parameters, and

(2) differences between replicates must be due to alignment errors, because two different alignments cannot both be correct.

MSAs in a resampled ensemble are derived from the same original sequences by sampling columns. Here, the sequence labels are the same as the originals, but letters are shuffled due to sampling.