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Run summary data
Master run log log_20130513121941.txt
BIOM table statistics biom_table_summary.txt
Filtered BIOM table (minimum sequence count: 20) table_mc20.biom.gz
Taxonomic summary results (by day)
Taxa summary bar plots bar_charts.html
Taxa summary area plots area_charts.html
Taxonomic summary results
Taxa summary bar plots bar_charts.html
Taxa summary area plots area_charts.html
Taxonomic summary results (by SampleType)
Taxa summary bar plots bar_charts.html
Taxa summary area plots area_charts.html
Category results
Category significance (SampleType) category_significance_SampleType.txt
Category significance (day) category_significance_day.txt
Alpha diversity results
Alpha rarefaction plots rarefaction_plots.html
Alpha diversity statistics (SampleType, chao1) SampleType_chao1.txt
Alpha diversity statistics (SampleType, observed_species) SampleType_observed_species.txt
Alpha diversity statistics (SampleType, PD_whole_tree) SampleType_PD_whole_tree.txt
Alpha diversity statistics (day, chao1) day_chao1.txt
Alpha diversity statistics (day, observed_species) day_observed_species.txt
Alpha diversity statistics (day, PD_whole_tree) day_PD_whole_tree.txt
Beta diversity results (even sampling: 20)
Distance boxplots (weighted_unifrac) SampleType_Distances.pdf
Distance boxplots statistics (weighted_unifrac) SampleType_Stats.txt
Distance boxplots (weighted_unifrac) day_Distances.pdf
Distance boxplots statistics (weighted_unifrac) day_Stats.txt
3D plot (weighted_unifrac, continuous coloring) weighted_unifrac_pc_3D_PCoA_plots.html
3D plot (weighted_unifrac, discrete coloring) weighted_unifrac_pc_3D_PCoA_plots.html
2D plot (weighted_unifrac, continuous coloring) weighted_unifrac_pc_2D_PCoA_plots.html
2D plot (weighted_unifrac, discrete coloring) weighted_unifrac_pc_2D_PCoA_plots.html
Distance matrix (weighted_unifrac) weighted_unifrac_dm.txt
Principal coordinate matrix (weighted_unifrac) weighted_unifrac_pc.txt
Distance boxplots (unweighted_unifrac) SampleType_Distances.pdf
Distance boxplots statistics (unweighted_unifrac) SampleType_Stats.txt
Distance boxplots (unweighted_unifrac) day_Distances.pdf
Distance boxplots statistics (unweighted_unifrac) day_Stats.txt
3D plot (unweighted_unifrac, continuous coloring) unweighted_unifrac_pc_3D_PCoA_plots.html
3D plot (unweighted_unifrac, discrete coloring) unweighted_unifrac_pc_3D_PCoA_plots.html
2D plot (unweighted_unifrac, continuous coloring) unweighted_unifrac_pc_2D_PCoA_plots.html
2D plot (unweighted_unifrac, discrete coloring) unweighted_unifrac_pc_2D_PCoA_plots.html
Distance matrix (unweighted_unifrac) unweighted_unifrac_dm.txt
Principal coordinate matrix (unweighted_unifrac) unweighted_unifrac_pc.txt

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See the QIIME tutorials for examples of additional analyses that can be run.
You can find documentation of the QIIME scripts in the QIIME script index.