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.

In memoriam.


Human language is a cracked kettle on which we beat out tunes for bears to dance to, when all the time we are longing to move the stars to pity.

— Gustave Flaubert, Madame Bovary

I regret to announce the untimely death Monday morning of Michael Farrar, principal software engineer for the Eddy lab. Michael was a critical part of our lab and an extraordinarily talented colleague. The lab is stunned. He is greatly, greatly missed. This will of course impact the HMMER3 development roadmap and our lab’s plans for the future. I will discuss business at some later time. Our thoughts now are with Michael’s wife and his three children.