> For the complete documentation index, see [llms.txt](https://docs.kbase.us/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.kbase.us/workflows/comparative-genomics/faq-comparative-genomics.md).

# FAQ: Comparative Genomics

## What does the `tail <1% each taxon` mean in the Kaiju output?

This option allows users to exclude rare lineages which would congest the plot. However, underlying analysis is not affected and the data can be replotted.

## Can I use the GTDB database within Kaiju?

Yes, you can run the our GTDB-tk Classify app on the same data as you run through Kaiju and compare. The GTDB-tk app is in the Microbial Communities section of the Apps Panel in the Narrative interface. One distinction: Kaiju runs on raw sequencing data (reads) and GTDB-tk works on assembled contigs.

## Does the Kaiju analysis give a text output that can be used in R, for example?

Yes, at the bottom of the App cell you can see an option to download kaiju\_classification.zip and kaiju\_summaries.zip which both contain text files.


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