A CONCEPT-type anvi’o artifact. This artifact is typically generated, used, and/or exported by anvi’o (and not provided by the user)..
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Required or used by
This is the output of anvi-compute-genome-similarity (which describes the level of similarity between all of the input genomes) or anvi-script-compute-ani-for-fasta (which describes the level of similarity between contigs in a fasta file).
The output of anvi-compute-genome-similarity will only be in this structure if you did not input a pan-db. Otherwise, the data will be put directly into the additional data tables of the pan-db. The same is true of anvi-script-compute-ani-for-fasta.
This is a directory (named by the user) that contains both a dendrogram (NEWICK-tree) and a matrix of the similarity scores between each pair for a variety of metrics dependent on the program that you used to run anvi-compute-genome-similarity or anvi-script-compute-ani-for-fasta .
For example, if you used
ANIb (the default program), the output directory will contain the following twelve files. These are directly created from the heatmaps generated by PyANI, just converted into matrices and newick files:
ANIb_alignment_coverage.txt: contains the percent coverage (for query and subject)
ANIb_percentage_identity.txt: contains the percent identity
ANIb_full_percentage_identity.txt: contains the percent identity in the context of the length of the entire query and subject sequences (not just the aligned segment)
ANIb_alignment_lengths.txt: contians the total aligned lengths
ANIb_similarity_errors.txt: contains similarity errors (total number of mismatches, not including indels)
ANIb_hadamard.txt: contians the hadamard matrix (dot product of identity and coverage matrices)
Edit this file to update this information.