Parameter Advising for Multiple Sequence Alignment

1 Introduction and Background.- 2 Alignment Accuracy Estimation.- 3 The Facet Estimator.- 4 Computational Complexity of Advising.- 5 Constructing Advisors.- 6 Parameter Advising for the Opal Aligner.- 7 Ensemble Mind Alignment.- 8 Adaptive Local Realignment.- 9 Core Column Prediction for Alignments.- 10 Future Directions.