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Run summary data
Master run log log_20150116193701.txt
Previous run log log_20150116192243.txt
BIOM table statistics biom_table_summary.txt
Filtered BIOM table (minimum sequence count: 1114) table_mc1114.biom.gz
Rarified BIOM table (sampling depth: 1114) table_even1114.biom.gz
Beta diversity results (even sampling: 1114)
Distance boxplots (weighted_unifrac) SampleType_Distances.pdf
Distance boxplots statistics (weighted_unifrac) SampleType_Stats.txt
Distance boxplots (weighted_unifrac) DaysSinceExperimentStart_Distances.pdf
Distance boxplots statistics (weighted_unifrac) DaysSinceExperimentStart_Stats.txt
PCoA plot (weighted_unifrac) index.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) DaysSinceExperimentStart_Distances.pdf
Distance boxplots statistics (unweighted_unifrac) DaysSinceExperimentStart_Stats.txt
PCoA plot (unweighted_unifrac) index.html
Distance matrix (unweighted_unifrac) unweighted_unifrac_dm.txt
Principal coordinate matrix (unweighted_unifrac) unweighted_unifrac_pc.txt
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
Taxonomic summary results (by DaysSinceExperimentStart)
Taxa summary bar plots bar_charts.html
Taxa summary area plots area_charts.html
Alpha diversity results
Alpha rarefaction plots rarefaction_plots.html
Alpha diversity statistics (SampleType, PD_whole_tree) SampleType_stats.txt
Alpha diversity boxplots (SampleType, PD_whole_tree) SampleType_boxplots.pdf
Alpha diversity statistics (DaysSinceExperimentStart, PD_whole_tree) DaysSinceExperimentStart_stats.txt
Alpha diversity boxplots (DaysSinceExperimentStart, PD_whole_tree) DaysSinceExperimentStart_boxplots.pdf
Alpha diversity statistics (SampleType, chao1) SampleType_stats.txt
Alpha diversity boxplots (SampleType, chao1) SampleType_boxplots.pdf
Alpha diversity statistics (DaysSinceExperimentStart, chao1) DaysSinceExperimentStart_stats.txt
Alpha diversity boxplots (DaysSinceExperimentStart, chao1) DaysSinceExperimentStart_boxplots.pdf
Alpha diversity statistics (SampleType, observed_otus) SampleType_stats.txt
Alpha diversity boxplots (SampleType, observed_otus) SampleType_boxplots.pdf
Alpha diversity statistics (DaysSinceExperimentStart, observed_otus) DaysSinceExperimentStart_stats.txt
Alpha diversity boxplots (DaysSinceExperimentStart, observed_otus) DaysSinceExperimentStart_boxplots.pdf
Group significance results
Category significance (SampleType) group_significance_SampleType.txt
Category significance (DaysSinceExperimentStart) group_significance_DaysSinceExperimentStart.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.