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Table 1 Comparison of different grouping algorithms available within FastGroupII and DOTUR. A total of 621 16S rDNA sequences were grouped 20 times using the PSI, PSI with Gaps, and Seq-Match methods. During each separate grouping, Query Sequences were chosen at random to determine if there was any effect of input order. Data from these 20 groupings are shown as the average ± standard deviation. The Tree-parsing and DOTUR methods use global alignments, so randomization was not used. The 3 methods in DOTUR use the PHYLIP distance matrix generated from a global alignment in ClustalW (FN: Furthest Neighbor, NN: Nearest Neighbor, AN: Average Neighbor).

From: FastGroupII: A web-based bioinformatics platform for analyses of large 16S rDNA libraries

  PSI PSI with Gaps Seq-Match Tree-parsing DOTUR
      FN NN AN
# of groups 209 ± 2 160 ± 4 140 ± 3 200 132 122 126
Richness (Chao1) 599 ± 27 359 ± 22 281 ± 8 440 249 241 246
Diversity (Shannon-Wiener) 3.98 ± 0.04 3.62 ± 0.10 3.35 ± 0.19 4.5 3.58 3.04 3.07
# of singletons 148 ± 2 99.7 ± 3.2 80.8 ± 1.7 120 72 69 71
# of doubletons 28.2 ± 1.5 25.3 ± 2.7 23.2 ± 0.9 29 22 20 21