anvi-script-checkm-tree-to-interactive

Authors
Requires
Provides
Usage
Command line interface

Command line usage
Parameters and their descriptions

Additional Resources

A helper script to convert CheckM trees into anvio interactive with taxonomy information.

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Authors

Özcan C. Esen

Requires

phylogeny

Provides

interactive

Usage

A helper script to process CheckM tree output to generate files compatible with anvi-interactive.

An example use:

anvi-script-checkm-tree-to-interactive -t CheckM_concatenated.tree \ -o OUTPUT_PATH cd OUTPUT_PATH/ anvi-interactive -p PROFILE.db \ -t newick.tree \ -d view_data.txt

Edit this file to update this information.

Command line interface

The following is the list of parameters and their descriptions in the latest version of anvi-script-checkm-tree-to-interactive.

The code that generates this web page ensures that this information is the latest available in 9-dev (eunice). Which means, in some cases the information in this section (generated automatically) might be more comprehensive or up-to-date compared to the descriptions above (written by humans).

Command line usage

anvi-script-checkm-tree-to-interactive [-h] -t CHECKM TREE -o DIRECTORY

Parameters and their descriptions

options

-t, --tree CHECKM TREE required: Tree file generated by CheckM.
-o, --output-dir DIRECTORY required: The directory name that output files will be stored.

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.