phylogeny

A NEWICK-type anvi’o artifact. This artifact can be generated, used, and/or exported by anvi’o. It can also be provided by the user for anvi’o to import into its databases, process, and/or use.

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Provided by

anvi-export-items-order anvi-gen-phylogenomic-tree

Required or used by

anvi-import-items-order anvi-import-misc-data anvi-interactive anvi-script-checkm-tree-to-interactive

Description

This is a NEWICK-formatted tree that describes the phylogenic relationships of your data.

Wondering what the NEWICK format is? Then you’re in luck! It has its own Wikipedia page.

How to get one of these?

You can use anvi-gen-phylogenomic-tree to create a phylogeny based on a series of genes.

As discussed on the page for anvi-gen-phylogenomic-tree, you can also use an external program to get a NEWICK-formatted tree and use that.

What can I do with it?

Firstly, you can use it to reorder elements of the interactive interface. To import this to rearrange the orders that your items appear (in other words, as the central phylogenetic tree when you open the interface), import it using anvi-import-items-order. To import this as a tree describing your layers (the concentric circles in the anvi’o interface), convert this to a misc-data-layer-orders-txt and use the program anvi-import-misc-data.

Secondly, as done in the Phylogenetics tutorial, you can open it in the interactive interface without an associated contigs-db. To do this, run anvi-interactive as so:

This will create an empty profile-db to store any bins you create and other such data. You can also add various information, such as taxonomy hits, as done in that same Phylogenetics tutorial.

Edit this file to update this information.