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Table 3. HSP overlap filtering and distance calculation.

From: Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs

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]  
  1. Evidence codes: [M] measured; [E] extrapolated.