A CONCEPT-type anvi’o artifact. This artifact is typically generated, used, and/or exported by anvi’o (and not provided by the user)..
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anvi-import-items-order anvi-merge anvi-pan-genome anvi-profile
There are no anvi’o tools that use or require this artifact directly, which means it is most likely an end-product for the user.
This artifact describes the order of items in visualization tasks.
In anvi’o, main display items (such as ‘gene clusters’ in a pan database, ‘contigs’ in a profile database, etc) can be ordered either by a NEWICK formatted tree (such as a phylogenetic tree or a hierarchical clustering dendrogram), or by an array (such as a flat list of item names).
When a NEWICK tree is used to order items, it will appear as the tree in the central section of the default anvi’o interactive interface. When a flat list of items are provided to order items, the central display where a tree appears will be blank and the displayed items will still be ordered according to the list. In order words, items order is to misc-data-items as misc-data-layer-orders is to misc-data-layers: a description not of the items themselves, but of what order they go in on the interface.
Anvi’o programs such as anvi-pan-genome, anvi-merge, and anvi-profile automatically generate NEWICK-formatted items order if possible (i.e., if you have less than 20,000 items). When you run these programs, they will put this information into your resulting pan-db or profile-db.
You can also export this information to give to a fellow anvi’o user or import this information if you have your own phylogenetic tree or desired order for your contigs.
You can use anvi-import-items-order to import specific orders for your items, or anvi-export-items-order to export this information.
Edit this file to update this information.