What are the options available to parse output (full output with alignments) from jackhmmer? As far as I can test, BioPerl hmmer module isn't able to read it correctly. Are there any ready-to-use libraries (language doesn't matter), or I should write something on my own?
Well, apparently the correct answer is that no library exists that parses full jackhmmer output. Its authors even write:
The output format is designed to be human-readable, but is often so voluminous that reading it is impractical, and parsing it is a pain. The --tblout and --domtblout options save output in simple tabular formats that are concise and easier to parse.
In case one needs sequences of hits, there are two options. One is to painfully write a parser. The other one is to extract sequence based on coordinates provided by tabular formats.