> For the complete documentation index, see [llms.txt](https://kb.ezbiocloud.net/home/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://kb.ezbiocloud.net/home/protocols/shotgun-microbiome/analyze-datasets/lefse.md).

# LEfSe

Let’s run a **LEfSe** analysis of the profiles in this dataset from the Parkinson’s disease study.

## Select ‘LEfSe’ <a href="#span-classeztocsection-idselecte28098lefsespanselect-lefse-span-classeztocsectionendspan" id="span-classeztocsection-idselecte28098lefsespanselect-lefse-span-classeztocsectionendspan"></a>

<figure><img src="/files/f5Yv1xE0QB9s0tqYmOt5" alt=""><figcaption></figcaption></figure>

## Select your dataset <a href="#span-classeztocsection-idselectyourdatasetspanselect-your-dataset-span-classeztocsectionendspan" id="span-classeztocsection-idselectyourdatasetspanselect-your-dataset-span-classeztocsectionendspan"></a>

<figure><img src="/files/WDvsqWtQoQrYxoj6g096" alt=""><figcaption></figcaption></figure>

## Fill in details for future referencing <a href="#span-classeztocsection-idfillindetailsforfuturereferencingspanfill-in-details-for-future-referencing" id="span-classeztocsection-idfillindetailsforfuturereferencingspanfill-in-details-for-future-referencing"></a>

## Input the arguments according to your desired output <a href="#span-classeztocsection-idinputtheargumentsaccordingtoyourdesiredoutputspaninput-the-arguments-accord" id="span-classeztocsection-idinputtheargumentsaccordingtoyourdesiredoutputspaninput-the-arguments-accord"></a>

<figure><img src="/files/A4phiNLEd8P2eZINRDfP" alt=""><figcaption></figcaption></figure>

## Select ‘Run Analysis’ <a href="#span-classeztocsection-idselecte28098runanalysisspanselect-run-analysisspan-classeztocsectionendspan" id="span-classeztocsection-idselecte28098runanalysisspanselect-run-analysisspan-classeztocsectionendspan"></a>

<figure><img src="/files/9vrzpH8zIIH4uFHafLS5" alt=""><figcaption></figcaption></figure>

## Wait for the analysis to complete <a href="#span-classeztocsection-idwaitfortheanalysistocompletespanwait-for-the-analysis-to-completespan-class" id="span-classeztocsection-idwaitfortheanalysistocompletespanwait-for-the-analysis-to-completespan-class"></a>

<figure><img src="/files/yA8legj5Mw3amI0eGmbb" alt=""><figcaption></figcaption></figure>

<figure><img src="/files/McpQtHYkX7PkWvOyUUOR" alt=""><figcaption></figcaption></figure>