Tree options (report option 3)

How to customise the trees produced in the civet report.

-ta/--tree-annotations

Comma separated string of metadata columns to annotate catchment trees with, can then be displayed in the report.


Default:
lineage,country


Usage:
--tree-annotations {$LIST} or -ta {$LIST}

-mt/--max-tree-size

Maximum number of sequences allowed in a given catchment tree. Catchments with more than this will be summarised in a table rather than a tree.


Default:
500


Usage:
--max-tree-size {$NUMBER} or -mt {$NUMBER}

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