Comparative Metagenomic Analysis of Human Gut Microbiome Composition Using Two Different Bioinformatic Pipelines

Table 2

Overview of all diversity analysis metrics and statistical tests available in MG-RAST and QIIME.

	Alpha diversity metrics*	Beta diversity metrics§	Statistical tests^†
MG-RAST	Shannon	Bray-Curtis	Unpaired 𝑡 test; ANOVA; Mann-Whitney test; Kruskal-Wallis test
	Nonphylogeny based metrics	Non-phylogeny based metrics
QIIME	berger_parker_d; brillouin_d; chao1; chao1_confidence; dominance; doubles; equitability; fisher_alpha; gini index; goods coverage; heip_e; kempton_taylor_q; margalef; mcintosh_d; mcintosh_e; menhinick; michaelis_menten_fit; observed_species; osd; robbins; Shannon; simpson (1-Dominance); simpson_reciprocal; (1/Dominance); simpson_e; singles; strong	abund_jaccard; binary_chisq; binary_chord; binary_euclidean; binary_hamming; binary_jaccard; binary_lennon; binary_ochiai; binary_otu_gain; binary_pearson; binary_sorensen_dice; bray_curtis; bray_curtis_faith; bray_curtis_magurran; canberra; chisq; chord; euclidean; gower; hellinger; kulczynski; manhattan; morisita_horn; pearson; soergel; spearman_approx; specprof	ANOVA; G-test; Paired 𝑡 test; Longitudinal correlation; two sample 𝑡 test; adonis; ANOSIM; BEST; Moran’s I; MRPP; PERMANOVA; PERMDISP; db-RDA; Mantel test
	Phylogeny based metrics	Phylogeny based metrics
	PD whole tree	unifrac; unifrac_g; unifrac_g_full_tree; unweighted_unifrac; unweighted_unifrac_full_tree; weighted_normalized_unifrac; weighted_unifrac

∗Alpha diversity metrics for both the tools; §beta diversity available metrics; ^†parametric and non-parametric statistical tests available by default in the two tools.