Run ANI between contigs in a single FASTA file.

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This program computes the average nucleotide identity between reads in a single fasta file (using PyANI).

To compute the ANI (or other genome distance metrics) between two genomes in different fasta files, use anvi-compute-genome-similarity.

A default run of this program looks like this:

anvi-script-compute-ani-for-fasta -f fasta \ -o path/to/output \ --method ANIb

By default, the PyANI method is ANIb (which aligns 1020 nt fragments of your sequences using BLASTN+). You can switch to ANIm, ANIblastall, or TETRA if desired. See the PyANI documentation for more informaiton.

You also have the option to change the distance metric (from the default “euclidean”) or the linkage method (from the default “ward”) or provide a path to a log file for debug messages.

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.