Table 1 Summary of results and performance on Salmonella data
From: A practical exact maximum compatibility algorithm for reconstruction of recent evolutionary history
Cluster number | Number of Genomes | Columns in Input | Maximum Compatible Set(s) | Ambiguities in Binary Columns | Columns Not Fully Disambiguated | Columns Represented on Tree | Execution time (sec.) | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Variable | Binary | Informative | Size | Number | Fraction Ambiguous States | Fraction of Columns with Ambiguities | Total | Informative and Non-redundant | Number | Fraction of variable | Fraction of binary | |||
1 | 1854 | 12237 | 12013 | 4933 | 11551 | 32 | 0.4% | 72.1% | 140.5 | 14 | 11410.5 | 93.2% | 95.0% | 9.77 |
2 | 1586 | 14229 | 14184 | 5851 | 13923 | 2 | 0.2% | 43.3% | 153 | 19 | 13770 | 96.8% | 97.1% | 3.92 |
3 | 943 | 7130 | 7121 | 2357 | 7032 | 2 | 1.4% | 23.7% | 168.5 | 2 | 6863.5 | 96.3% | 96.4% | 1.4 |
4 | 843 | 2439 | 2434 | 1206 | 2404 | 2 | 0.3% | 8.9% | 11 | 0 | 2393 | 98.1% | 98.3% | 0.48 |
5 | 826 | 6143 | 6134 | 1964 | 6014 | 1 | 0.9% | 53.6% | 189 | 3 | 5825 | 94.8% | 95.0% | 1.34 |
6 | 818 | 8271 | 8257 | 2524 | 8182 | 1 | 0.5% | 41.1% | 190 | 36 | 7992 | 96.6% | 96.8% | 1.43 |
7 | 450 | 6031 | 6023 | 2158 | 5973 | 2 | 0.7% | 42.6% | 93 | 0 | 5880 | 97.5% | 97.6% | 0.74 |
8 | 403 | 6323 | 6317 | 2386 | 6278 | 1 | 0.7% | 39.5% | 76 | 0 | 6202 | 98.1% | 98.2% | 0.6 |
9 | 379 | 5171 | 5164 | 1714 | 5002 | 1 | 1.2% | 56.4% | 148 | 0 | 4854 | 93.9% | 94.0% | 0.78 |
10 | 278 | 1156 | 1156 | 405 | 1145 | 1 | 0.6% | 10.6% | 8 | 1 | 1137 | 98.4% | 98.4% | 0.26 |
11 | 259 | 4223 | 4221 | 1279 | 4201 | 2 | 0.4% | 10.6% | 24 | 0 | 4177 | 98.9% | 99.0% | 0.35 |
12 | 215 | 3538 | 3533 | 1202 | 3517 | 1 | 0.8% | 16.4% | 39 | 1 | 3478 | 98.3% | 98.4% | 0.33 |
13 | 210 | 2879 | 2867 | 687 | 2824 | 2 | 0.7% | 11.1% | 18 | 0 | 2806 | 97.5% | 97.9% | 0.29 |
14 | 195 | 2697 | 2695 | 1223 | 2684 | 1 | 1.8% | 44.4% | 52 | 0 | 2632 | 97.6% | 97.7% | 0.42 |
15 | 193 | 2086 | 2084 | 786 | 2065 | 2 | 1.1% | 12.4% | 39 | 0.5 | 2026 | 97.1% | 97.2% | 0.46 |
16 | 192 | 903 | 902 | 276 | 874 | 4 | 4.7% | 23.5% | 47.5 | 3 | 826.5 | 91.5% | 91.6% | 0.26 |
17 | 190 | 2640 | 2638 | 984 | 2603 | 1 | 1.4% | 12.0% | 51 | 2 | 2552 | 96.7% | 96.7% | 0.29 |
18 | 171 | 1035 | 1033 | 353 | 1023 | 1 | 0.5% | 8.2% | 6 | 0 | 1017 | 98.3% | 98.5% | 0.23 |
19 | 171 | 979 | 979 | 337 | 968 | 1 | 1.7% | 21.2% | 30 | 2 | 938 | 95.8% | 95.8% | 0.26 |
20 | 168 | 2738 | 2738 | 612 | 2708 | 1 | 1.3% | 11.9% | 44 | 1 | 2664 | 97.3% | 97.3% | 0.28 |