I ran nhmmer to see if/where a certain gene was found in a fungi genome. The results of this query give me a .out file that contains multiple gene sequences that are part of a hit.
However, the results of this hit are very unorganized. They are interspersed with other information about the alignment sequences, they aren't linked together, and there are long headers and footers on the file.
Is there a command I can use through hmmer or esl-reformat or esl-sfetch to extract a fasta file from this .out file with just the hit sequences?