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fixup: fix code block format
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joverlee521 committed Apr 7, 2022
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Expand Up @@ -14,6 +14,7 @@ Exclude sites
Augur tree allows you to mask certain problematic sites before tree-building via `augur tree --exclude-sites <exclude_file> --alignment <alignment>` , where each line in `<exclude_file>` is a 1-based nucleotide position to mask from the alignment. We can recreate this via the following command:

.. code-block:: bash
augur mask --sequences <alignment> --mask <exclude_file> --output <masked_alignment>
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