Microbial 'omics

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hmm-hits-matrix-txt [artifact]

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A TXT-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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There are no anvi’o tools that use or require this artifact directly, which means it is most likely an end-product for the user.


This file is the output of anvi-script-gen-hmm-hits-matrix-across-genomes and describes the hmm-hits across multiple genomes or bins for a single hmm-source.

The first column describes each of the genomes (if the input was an external-genomes) or bins (if the input was an internal-genomes) that the matrix describes. The following columns describe each of the genes in your hmm-source. The data within the table describes the number of hits that gene had in that genome or bin.

For example, if you were to run anvi-script-gen-hmm-hits-matrix-across-genomes with the Bacteria_71 hmm-source on two hypothetical genomes, you would get a file like this:

genome_or_bin    ADK    AICARFT_IMPCHas    ATP-synt    ATP-synt_A    Adenylsucc_synt    Chorismate_synt    EF_TS    ...
Genome_1         11     10                 9           9             11                 8                  9        ...
Genome_2         2      1                  1           2             3                  2                  2        ...

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