Smoothed Bootstrap Aggregation for Assessing Selection Pressure at Amino Acid Sites

We present an alternative to BEB called smoothed bootstrap aggregation (SBA), which bootstraps site patterns from an alignment of protein coding DNA sequences to accommodate the uncertainty in the parameter estimates. We show that deriving the correction for parameter uncertainty from the data in hand, in combination with kernel smoothing techniques, improves site specific inference of positive selection. We compare BEB to SBA by simulation and real data analysis. Simulation results show that SBA balances accuracy and power at least as well as BEB, and when parameter estimates are unstable, the performance gap between BEB and SBA can widen in favor of SBA. SBA is applicable to a wide variety of other inference problems in molecular evolution.

Source: Molecular Biology and Evolution - October 12, 2016 Category: Molecular Biology Authors: Mingrone, J., Susko, E., Bielawski, J. Tags: Methods Source Type: research