Microbial 'omics


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anvi-matrix-to-newick [program]

Takes a distance matrix, returns a newick tree.

See program help menu or go back to the main page of anvi’o programs and artifacts.

Table of Contents

Can provide

dendrogram

Can consume

view-data

Usage

This program converts a distance matrix (computed from a view-data artifact) into a dendrogram.

It uses the numerical data in a view-data to compute a distance matrix behind the scenes, and then runs some hierarchical clustering to create a dendrogram for all of your items.

With all default parameters, a run would look like this:

anvi-matrix-to-newick -o path/for/dendrogram \ view-data

If your input file has your samples as rows instead of columns, just add the flag --transpose.

You can also ask for an additional output file: the order of the items in the resulting dendrogram as a misc-data-items-order in LIST format. To get this, simply provide a path to its desired location with --items-order-file.

Additionally, for hierarchical clustering, you can change the distance metric (a full list of the available metrics can be found here) or the linkage method (though this is not recommended, the list of options can be found here).

Edit this file to update this information.

Additional Resources

Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the __resources__ tag in this file to see an example.