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Copy file name to clipboardexpand all lines: docs/src/commands/de_novo_wf.rst
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The *de novo* workflow infers new bacterial and archaeal trees containing all user supplied and GTDB-Tk reference genomes.
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The classify workflow is recommended for obtaining taxonomic classifications, and this workflow only recommended if
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a *de novo* domain-specific trees are desired.
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a *de novo* domain-specific trees are desired. **One should take the taxonomic assignments as a guide, but not as final classifications**. In particular, no effort is made to resolve the taxonomic assignment of lineages composed exclusively of user submitted genomes.
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This workflow consists of five steps: ``identify``, ``align``, ``infer``, ``root``,
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