Table 2. Primary parameters under control in the sweep.
In total, each clustering algorithm is presented with 600 combinations which may further increase depending on whether a clustering algorithm also has runtime parameters under control.
| Level | Name | Description | Type | Number | Total | Values |
|---|---|---|---|---|---|---|
| 1 | tree | Phylogenetic tree topology | factor | 2 | 2 | star, ladder |
| 2 | profile | Relative abundance profile | factor | 2 | 4 | uniform, 1∕e |
| 3 | αBL | Branch length scale factor | numeric | 10 | 40 | 0.025–1 (log scale) |
| 4 | xfold | WGS paired-end depth of coverage | numeric | 3 | 120 | 10, 50, 100 |
| 5 | n3c | Number of 3C read-pairs | numeric | 5 | 600 | 10000, 20000, 50000, 100000, 1000000 |
| 6 | algo | Clustering algorithm | factor | 5 | MCL, SM-MCL, Louvain-hard, Louvain-soft, OClustR |