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.

Jiang et al. BMC Genomics 2012 13:730   doi:10.1186/1471-2164-13-730

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