Table 2 Scalability benchmark through the viral nucleotide and amino acid sequence datasets
From: Clustering biological sequences with dynamic sequence similarity threshold
| Â | Datasets | |||||
|---|---|---|---|---|---|---|
Viral nucleotides (≤ 10,000 nts) | Long viral nucleotides (> 10,000 nts) | Viral amino acids@ | ||||
No. of clusters | Time (hh:mm:ss) | No. of clusters | Time (hh:mm:ss) | No. of clusters | Time (hh:mm:ss) | |
ALFATClust$ | 237,276 | 00:35:41 | 499 | 00:00:39 | 234,451 | 00:27:23 |
CD-HIT | N.A.# | 506 | 00:16:10 | 109,515 | 04:29:06 | |
UCLUST | 245,658 | 07:47:25 | N.A.* | 243,982 | 00:00:56 | |
MMseqs2 | 221,997 | 00:02:18 | 428 | 00:00:15 | 235,921 | 00:06:43 |
VSEARCH | 239,728 | 05:23:11 | 507 | 01:48:36 | Â | Â |
MeShClust | 8713 | 00:14:53 | 462 | 01:14:52 | Â | Â |
MeShClust2 | 194,267 | 03:43:00 | 571 | 00:00:10 | Â | Â |
DNACLUST | N.A.^ | N.A.^ | Â | Â | ||