Table 2 |
|||||||||
| Parsimony scores on the clustering tree of 23 open ocean samples belonging to 4 groups (Sargasso Sea, Caribbean Sea, Eastern Tropical Pacific and Tropical South Pacific) obtained by sequence signature methods using different dissimilarity measures based on the open ocean metagenomics data | |||||||||
| k | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 |
| d2 | 6 | 6 | 6 | 7 | 7 | 7 | 7 | 7 | 6 |
| d2S|M0 | 5 | 6 | 5 | 4 | 4 | 4 | 4 | 4 | 5 |
| d2S|M1 | 11 | 6 | 5 | 6 | 5 | 5 | 6 | 5 | 4 |
| d2S|M2 | NA | 8 | 4 | 6 | 5 | 5 | 5 | 5 | 5 |
| d2S|M3 | NA | NA | 5 | 6 | 6 | 5 | 6 | 5 | 5 |
| d2*|M0 | 5 | 5 | 4 | 4 | 6 | 6 | 6 | 7 | 7 |
| d2*|M1 | 9 | 7 | 7 | 5 | 6 | 6 | 6 | 7 | 7 |
| d2*|M2 | NA | 8 | 7 | 5 | 5 | 5 | 7 | 6 | 7 |
| d2*|M3 | NA | NA | 6 | 5 | 5 | 5 | 7 | 7 | 6 |
| Ma | 6 | 5 | 5 | 5 | 5 | 4 | 4 | 5 | 4 |
| Eu | 6 | 6 | 5 | 6 | 8 | 7 | 7 | 7 | 7 |
| Ch | 7 | 7 | 8 | 9 | 9 | 7 | 7 | 6 | 6 |
| Hao | NA | 5 | 6 | 6 | 6 | 6 | 4 | 5 | 6 |
| Willner | 7 | 6 | 5 | ||||||
The “Mi” indicates that the expected counts are calculated based on i-th order Markov model for the background sequences. Monte Carlo p-values were estimated by comparing observed parsimony score to the scores in 10000 random joined trees: parsimony score = 4--6, p < 0.001; score = 7, p = 0.004; score = 8; p = 0.003; score = 9; p = 0.12. Boldfaced are the two lowest parsimony scores.
Jiang et al. BMC Genomics 2012 13:730 doi:10.1186/1471-2164-13-730
