Table 1.

Computation Times for Large Alignments of Viral Genomes.

Gene/Genome	Number of Distinct Sequences	Sequence Length (nt)	Number of Polymorphic Sites	% of Triplets with Exact P Values	Dunn–Sidak Corrected P Value	Number of Identified Recombinant Sequences Longer Than 500 nt	Run Time
Avian influenza A/H5N1. PB2 segment	112	2,409	844	100	0.0016	0	11 s
Avian influenza A/H5N1, NS segment	160	906	298	100	1	0	24 s
MERS-CoV, whole genome	164	30,130	1,150	100	1.72×10−11	100	1.5 min
Zika virus, whole genome	157	11,192	2,792	>99.9	1.44×10−37	6	2 min
Ebola virus, 2013–2015 epidemic, whole genome	982	18,980	2,535	100	6.49×10−12	0	8.5 h
Dengue virus, serotype 2, whole genome	1,108	11,349	6,151	99.4	0	36	15.5 h

Note.—Computations were done on a 2.6-GHz linux laptop with 16-GB RAM. The P value table used was 1,200 × 1,200 × 1,200, which has a memory footprint of 2.2 GB.