Type the following command:

*\$ python /path/to/metaphlan2.py /path/to/textile\_microbiome.fastq.gz --input\_type fastq > textile\_microbiome \_profile.txt*

*Metagenomics-Based Phylogeny and Phylogenomic DOI: http://dx.doi.org/10.5772/intechopen.89492*


*The taxonomic levels are: Kingdom, k; and Phylum, p. The table was trimmed to show only up to the phylum level; to read complete report, see [7].*

#### **Table 2.**

*Features of the abundance table for a textile dye degrader microbiome profile.*


## **# Input files**


Finally, you will obtain:


You can change the format of the final results to pdf, just modifying the name: *merged\_abundance.png* to *merged\_abundance.pdf* in the last command. A representation of the annotated cladogram is shown in **Figure 2**. The size of the nodes correlates with microbial community relative abundances.

**Figure 2.**

*Cladogram produced by GraPhlAn software with metadata from MetaPhlan community profiling to order level. Taxon abundance is proportional to the circle diameter.*
