Table 1

Parsimony scores on the clustering of the three mammalian groups (hindgut-fermenting herbivores, foregut-fermenting herbivores and simple-gut) obtained by sequence signature methods using different dissimilarity measures based on the metagenomic data
k 2 3 4 5 6 7 8 9 10
d2 7 5 5 5 5 5 6 6 5
d2S|M0 5 3 3 2 4 4 4 4 6
d2S|M1 9 4 3 4 4 4 4 5 7
d2S|M2 NA 4 3 5 4 4 4 4 6
d2S|M3 NA NA 3 4 4 5 4 4 7
d2*|M0 7 7 6 4 5 4 4 6 7
d2*|M1 8 5 4 4 5 5 5 6 7
d2*|M2 NA 4 5 5 5 5 6 6 7
d2*|M3 NA NA 4 4 5 5 5 5 6
Ma 7 5 5 5 5 5 5 4 6
Eu 7 5 5 5 5 5 5 7 5
Ch 7 6 5 5 5 4 5 6 7
Hao NA 5 4 4 6 6 8 9 11
Willner 11 10 8

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 1000 randomly-joined trees: parsimony score = 2--7, p < 0.001; score = 8, p = 0.002. 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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