BioMed Research International / 2014 / Article / Tab 2 / Research Article
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
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
test Longitudinal correlation two sample
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.