Table 1.
Parameters used in sequence–sequence clustering grid search.
| Parameter name | Values | Brief description |
|---|---|---|
| —cluster-mode | 0, 1, 2 | Clustering algorithm to usea |
| —cluster-steps | 1, 2, 3 | Number of cascaded clustering steps to dob |
| −s | 1, 4, 7 | Sensitivityc |
| —min-seq-id | 0.5, 0.45, 0.4, 0.35, 0.3 | Percent identity threshold |
| −c | 0.9, 0.85, 0.8, 0.75, 0.7 | Coverage threshold |
| −e | 1e−10, 1e−05, 1e−3 | E-value threshold |
a
Different algorithms are available to interpret the graph of pairwise edges into clusters. 0 = set cover, 1 = single-linkage (like blastclust), 2 = greedy-incremental (like CD-HIT). Details are in MMseqs2 manual.
b
Performs clustering with strict parameters, then incrementally merges clusters by relaxing parameters down to the selected ones in these many steps.
c
Higher sensitivity values allow less similar k-mers to count as matches that can seed an alignment.