hmm-list

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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Provided by

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.

Required or used by

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.

Description

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 genes.txt
• 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:

name	source	path
Ribosomal_L16	Bacteria_71	INTERNAL
Ribosomal_S2	Bacteria_71	INTERNAL

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.

Here is what the hmm_list.txt should look like with a combination of internal and external hmm-sources:

name	source	path
Ribosomal_L16	Bacteria_71	INTERNAL
Ribosomal_S2	Bacteria_71	INTERNAL
RuBisCO_large	RuBisCO_large_HMM	PATH/TO/RuBisCO_large_HMM/

Edit this file to update this information.