Updated user guide

I’ve added some sections to the version of the HMMER User’s Guide that’s linked at hmmer.org. You can download the new Guide from here.

The Guide now briefly describes the HMMER3 acceleration pipeline for profile/sequence comparison, and the methods used to identify domain “envelopes”, maximum expected accuracy alignments, and posterior probabilities of aligned residue confidence. The Guide also now documents the --tblout and --domtblout tabular output formats.

This should help address questions about what all the fiddly columns mean in these outputs, especially in --tblout.

This version of the Guide included in HMMER distro tarballs is still the old version. The updated Guide will appear in distro tarballs for 3.1, which is coming Real Soon Now.


  1. hello sir,
    I want to know can I build a database of many .HMM files so that I can directly search my all genomic CDSs in a go with that database. If yes, how can i do this?
    Thanks in anticipation.



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