Table 5.

Results on GISAID catalogs

Pipeline	$mi{n}_{\mathit{lin}}$	$ma{x}_{\mathit{lin}}$	Min support	Precision	Recall	Time (s)	No. of correct lineages
A	5	20	2	.953	.947	38	40
A	5	20	5	.951	.945	19	40
B	5	20	2	.992	.967	48	40
B	5	20	5	.993	.960	21	40
A	50	50	2	.933	.918	897	40
A	50	50	5	.942	.948	355	40
B	50	50	2	.960	.962	2465	40
B	50	50	5	.972	.960	677	40

For each catalog, we report the precision and recall achieved by MALVIRUS in genotyping its variations, the average running times, and the number of input samples (out of 41) assigned to the correct lineage. We considered 8 different catalogs, built using pipeline A or B on the set of assemblies retrieved from GISAID, prefiltered using ${\tau }_N=5\%$ and then subsampled using different combinations of parameters $mi{n}_{\mathit{lin}}$ and $ma{x}_{\mathit{lin}}$. In addition, we also filtered out from the catalogs all variations present in less than either 2 or 5 assemblies (Min support columns)