Table 4.
Duration of distance calculation. Duration of the distance calculation step for two variants of the pattern-based method (dPB-ML, dPB-SIM). We present the time (measured in seconds) averaged over 100 sets of sequences in any given reference set (sets with the lowest/ highest phylogenetic distances from the synthetic data sets are used) encoded using two alphabets A. The hardware consisted of a 64-bit 2.4-GHz x86-compatible Intel processor.
| Control | ASRV | Short-sequences | |||||
|---|---|---|---|---|---|---|---|
|
|
|
|
|||||
| Method |
|
Set 1 | Set 7 | Set 1 | Set 7 | Set 1 | Set 7 |
| d PB-ML | CE | 1084 | 1045 | 864 | 1172 | 103.7 | 87.3 |
| d PB-SIM | CE | 81.1 | 97.3 | 63.4 | 103.6 | 7.10 | 7.46 |
| d PB-ML | AA | 76.2 | 36.0 | 97.2 | 68.9 | 11.77 | 3.24 |
| d PB-SIM | AA | 5.33 | 3.62 | 5.77 | 5.26 | 0.79 | 0.39 |