Table 3. Comparison of guide tree construction algorithms on extHomFam.
| Algorithm | small | medium | large | extra-large | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 200 < k ≤ 4000 | 4000 < k ≤ 10000 | 10000 < k < ≤ 25000 | 25000 < k ≤ 415519 | All | |||||||||||
| 113 families |
101 families |
96 families |
70 families |
380 families |
|||||||||||
| SP | TC | time | SP | TC | time | SP | TC | time | SP | TC | time | SP | TC | time | |
| FAMSA + single linkage | 82.9 | 71.5 | 1:31 | 82.8 | 71.9 | 8:14 | 76.1 | 60.8 | 29:50 | 66.3 | 47.7 | 6:19:10 | 78.1 | 64.5 | 6:58:45 |
| FAMSA + UPGMA | 83.6 | 72.6 | 1:09 | 80.8 | 69.0 | 6:50 | 73.6 | 56.8 | 28:29 | 64.2 | 45.6 | 6:42:14 | 76.8 | 62.7 | 7:18:42 |
| FAMSA + chained | 77.4 | 66.1 | 2:50 | 74.6 | 62.1 | 17:16 | 64.6 | 48.7 | 45:25 | 53.6 | 35.4 | 3:58:40 | 69.0 | 55.0 | 5:04:11 |
| FAMSA + Clustal Omega trees | 79.9 | 67.5 | — | 78.9 | 66.1 | — | 72.0 | 55.3 | — | 60.0 | 38.8 | — | 74.0 | 58.8 | — |
Times are provided in the hours:minutes:seconds format. The largest family (ABC_tran) was analyzed using the single linkage instead of UPGMA due to memory requirements.