A TXT-type anvi’o artifact. This artifact is typically provided by the user for anvi’o to import into its databases, process, and/or use.
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There are no anvi’o tools that generate this artifact, which means it is most likely provided to the anvi’o ecosystem by the user.
The hmm-list file is a TAB-delimited file with at least three columns:
name: The name of the HMM. If you are using an external HMM it MUST match the name found in the
source: Name of the collection of HMMs the HMM is found in e.g. Bacterial_71. If you are using an external HMM, simply put the name of the directory.
path: If using an Default HMM sources simply put “INTERNAL”. On the other hand, if you are using a user-defined HMM sources please put the full path to the anvi’o formatted HMM directory.
Here is an example of an hmm-list using the HMM Ribosomal_L16 and Ribosomal_S2 from the internal anvi’o collection Bacteria_71:
You can also use external hmm-sources! An easy way to get an anvi’o ready HMM directory is to use the script anvi-script-pfam-accessions-to-hmms-directory to download a Pfam HMM.
anvi-script-pfam-accessions-to-hmms-directory --pfam-accessions-list PF00016 -O RuBisCO_large_HMM
Here is what the
hmm_list.txt should look like with a combination of internal and external hmm-sources:
Edit this file to update this information.