Table 2.

ARPIP performance in simulation. All metrics include the root sequences and have been computed for each sample individually. We report the averages over the samples

Metric	Consistency (%)
Proportion of correctly inferred ancestral characters	$97.88\pm 2.01$
Proportion of correctly inferred ancestral columns	$90.35\pm 2.01$
Proportion of correctly inferred ancestral amino acids (i.e., excluding gaps)	$97.75\pm 2.55$
Gap precision	$94.27\pm 5.37$
Gap recall (sensitivity)	$96.99\pm 3.97$
Gap F-score	$95.46\pm 3.37$
Gap specificity	$99.29\pm 1.17$