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.

One Comment

  1. I think it would be better if the -tblout option was just an on/off option instead of supplying it a filename. Currently, if you use this option you still get the original output coming out of stdout, which seems kind of confusing. It would seem more intuitive for the std out to contain the new format if that option was selected. I guess some people might want to capture both types of output, but I think that would be a very rare case. Just my two cents!



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