Figure 3

Comparison of the covariance estimator and the ML variance estimator with their Monte Carlo counterparts. Error-bars indicate 95% confidence intervals. a) Monte Carlo covariance estimator vs. average of the covariance estimator for sequence lengths of {200, 500, 800} AA. In the dependence case, the estimator appears unbiased in most cases. In the independence case, the estimator shows a slight upward bias, but the absolute values are close to zero. In the triplet case, a downward bias with increasing covariance is visible. b) Monte Carlo variance estimator vs. average of ML variance estimator. A downward bias with increasing variance is visible.