A CONCEPT-type anvi’o artifact. This artifact is typically generated, used, and/or exported by anvi’o (and not provided by the user)..
Back to the main page of anvi’o programs and artifacts.
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.
Edit this file to update this information.