Article Figures & Data
Figures
- FIG. 1.
Description and comparison of the eight samples analyzed by Sogin et al. (27). The dendrogram to the left represents the similarity of the samples based on the membership-based Jaccard coefficient calculated using Chao1 estimated richness values. The dendrogram on the right represents the similarity of the samples based on the structure-based θYC coefficient. The distance from the tip of the dendrogram to the root is 0.50 for both trees.
- FIG. 2.
Rarefaction curves describing the dependence of discovering novel OTUs as a function of sampling effort for OTUs defined at a 0.10 distance cutoff. The curves for FS312 and FS396 climb to 3,095 and 2,804 OTUs after sampling of 54,894 and 80,769 sequences, respectively.
Tables
- TABLE 1.
Features from preexisting software that have been integrated into mothura
Existing tool Description Implementation in mothur Reference(s) Pyrosequencing pipeline (RDP) Online tool that trims and deconvolutes sequences using user-supplied data Stand-alone implementation; increased speed; greater flexibility; additional screening options 3 NAST, SINA, and RDP aligners Online tools that align user-supplied sequences with specific databases Stand-alone implementation; can utilize multiple processors; increased speed; greater flexibility; open source 3-5, 20 DNADIST Calculates pairwise distances between sequences (does not penalize for gaps) Can utilize multiple processors; more efficient use of RAM; various ways to penalize gaps 6 DOTUR and CD-HIT Assigns sequences to OTUs, constructs sampling curves, and estimates richness and diversity More efficient clustering; requires less memory; additional calculators; greater flexibility 10, 22 SONS Calculates estimates of the fraction and richness of OTUs shared between communities Generates dendrograms, heat maps, and Venn diagrams; additional calculators; greater flexibility 23 ∫-LIBSHUFF Uses the Cramer-von Mises statistic to test whether two communities have the same structure Eliminates the need for a sorted distance matrix; can specify pairwise comparisons 25, 26 TreeClimber Uses a parsimony-based test to determine whether two or more communities have the same structure Greater flexibility; can specify pairwise comparisons 14, 15, 24 UniFrac Compares the phylogenetic distance between communities to detect differences in community structure Stand-alone implementation; greater flexibility; can input bootstrap trees 12 ↵ a In all cases, modifications have been made to the mothur implementation of the algorithms for greater flexibility, speed, and resource utilization.
- TABLE 2.
Measures of α diversity for the samples characterized by Sogin et al. (27) for three OTU definitionsa
Sample No. of reads 0.03 0.05 0.10 OTU Chao H′ OTU Chao H′ OTU Chao H′ 53R 12,725 1,599 3,222 5.29 1,420 2,622 5.19 1,053 1,733 4.81 55R 9,848 1,469 2,994 5.54 1,302 2,496 5.43 962 1,741 5.03 112R 15,057 2,258 5,189 5.91 2,032 4,282 5.79 1,584 2,992 5.44 115R 16,181 1,749 3,600 5.31 1,552 3,088 5.21 1,135 1,919 4.83 137 13,831 1,425 2,687 5.44 1,295 2,430 5.36 989 1,645 5.07 138 12,938 1,425 2,542 5.24 1,253 2,131 5.14 957 1,479 4.81 FS312 54,894 4,371 10,691 5.23 3,948 9,259 5.16 3,095 6,409 4.94 FS396 80,769 4,359 10,208 4.67 3,806 8,609 4.60 2,804 5,437 4.42 ↵ a 0.03, 0.05, and 0.10 are the OTU cutoffs in distance units. OTU signifies the number of OTUs observed, Chao signifies the Chao1 estimated minimum number of OTUs, and H′ signifies the nonparametric Shannon diversity index.
