Some bugs crept through testing and into the 3.0b1 release of HMMER3. They're fixed, and the link in the "3.0b1" release post below was quietly updated to the 3.0b2 tarball available for download on our FTP site.

I fixed a bug with the new code that deals with fragment-rich alignments (sometimes hmmbuild was failing, complaining about a failed "trace validation"). I also added the --tblout and --domtblout options to hmmscan, which should've been there in the first place.