I want to generate a file that contains multiple HMMs, one each for given genes. HMMER documentation says this can be done, if created from a file containing more than one multiple sequence alignments. Further in HMMER docs, it says that a multiple MSA file must be in "Stockholm format," as the writers did not know of another format that could allow for a multiple MSA file.
HMMER can produce Stockholm-formatted MSAs, but it creates them from HMMs, not from actual reads. Creating Stockholm-formatted MSAs with HMMER from an HMM that wasn't produced from a Stockholm-formatted MSA also loses out on the important Stockholm-format MSA headers, so this approach did not work.
My goal is to use HMMER to query HMMs for multiple genes simultaneously or iteratively without needing to specify many different file names. I do not believe i can simply concatenate HMM files, either.
Can anyone suggest a way to produce an MSA in Stockholm format from reads or to work around this problem altogether?