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
--domtblout tabular output formats.
This should help address questions about what all the fiddly columns mean in these outputs, especially in
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.