Table 3. HSP overlap filtering and distance calculation.
HSP overlap filtering | |||
|---|---|---|---|
Algorithm/implementation | no filtering (coverage functions, see [1]) | HSP overlap filtering using the greedy-with-trimming approach described in [1] | |
Typical effect on correlation with DDH values | decrease (except for MUMmer) [M] | increase [M] | |
Distance calculation | |||
Ratio | Length HSPs per total genome length (1) | Number of identities within HSPs per total HSP length (2) | Number of identities within HSPs per total genome length (3) |
Typical effect on correlation with DDH values | increase [M] | moderate decrease; considerable decrease for MUMmer [M] | increase [M] |
Estimation of total genome length | Minimum | Average | |
Typical effect on correlation with DDH values | insignificant [M] | insignificant [M] | |
Use logarithm | Yes | No | |
Typical effect on correlation with DDH values | no effect [M] | no effect [M] |