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docs/user/PangenomeAnalyses/pangenomeWorkflow.md

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 The command has only one mandatory option, and predefined parameters adapted to pangenomes at the scale of a bacterial species.
 This command launches the [annotation](./pangenomeAnalyses.md#annotation), [clustering](./pangenomeCluster.md#cluster-genes-into-gene-families), [graph](./pangenomeAnalyses.md#graph) and [partition](./pangenomeAnalyses.md#partition) commands described below.
 
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 ```{mermaid}
 
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 ```
 
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 To use this command, you need to provide a tab-separated list of either annotation files (gff3 or gbff) or fasta files. The expected format is detailed [in the annotation section](./pangenomeAnalyses.md#annotation)