anvi-matrix-to-newick [program]
Table of Contents
Takes a distance matrix, returns a newick tree.
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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
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