# Analyzing PICRUSt predicted metagenomes¶

Once you have your PICRUSt metagenome predictions (see Metagenome Prediction Tutorial), you can analyze your predicted metagenomes as you would analyze actual metagenomes.

Here are some recommendations using both PICRUSt commands and other external tools:

## Collapse predictions into pathways¶

- Collapse the thousands of predicted functions into higher categories (e.g KOs into KEGG Pathways).
- See PICRUSt’s categorize_by_function.py.

## Determine which OTUs are contributing to particular functions¶

- Identify which OTUs are contributing which functions .
- See PICRUSt’s metagenome_contributions.py.

## Analyze with QIIME¶

- Compute alpha diversity, beta diversity, generate various plots, and much more using QIIME.
- See Analyzing metagenomes with QIIME.

## Analyze with STAMP¶

- Browse results, create PCA and bar plots, and make statistical inferences between pairs of samples or multiple groups all within a graphical interface using STAMP.
- See Analyzing metagenomes with STAMP.