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Table 2 OTU sets closest to the annotated species clustering for each multiple sequence alignment.

From: Alignment and clustering of phylogenetic markers - implications for microbial diversity studies

  Correction MSA Clustering Distance OTUs Ace Chao1 Shannon VI
  F84 ClustalW fn 0.05 56 79 116 3.39 0.044
Optimal F84 NAST fn 0.06 56 78 176 3.39 0.054
  JC MUSCLE fn 0.06 54 69 132 3.37 0.068
Drosophila (host) [36] JC ClustalW fn 0.03 70 109 162 3.49 0.087
Marine sponge [37] F84 ClustalW fn 0.03 70 109 162 3.49 0.087
Soil [11] JC NAST fn 0.03 99 150 169 3.66 0.157
Deep sea biosphere [13, 38] JC MUSCLE fn 0.03 96 396 466 4.66 0.190
Termite hindgut [39] JC NAST fn 0.01 185 360 351 4.11 0.320
  1. The "VI" column indicates the VI distance of each clustering from the annotated species clustering. Best methods chosen by our validation methodology for each MSA ("Optimal") are contrasted with five recently published methodologies. The "Correction" column corresponds to the evolutionary distance correction. Note that for the optimal methods using ClustalW and NAST alignments, the F84 and K2P corrections produced identical OTU sets because the distance matrices were very similar, though not identical. All methods in this table used furthest neighbor (fn) clustering. The Ace, Chao1, and Shannon diversity estimators are also provided.