Three of many possible reasons why I haven’t responded to your email about HMMER.

My relationship with email is fraught. On the one hand, it ravages my time and concentration; on the other hand, it’s better than the damned phone.

I get too much email to answer, and that makes me feel guilty. Would it help to post a general disclaimer? Often I think so. Many people post disclaimers about their email irresponsibility. Neal Stephenson’s is a spectacularly gruff example. I totally agree with Stephenson that I need “vast, unbroken slabs of time” to do anything substantive, but I don’t want to growl quite that much at people. Donald Knuth is inaccessible to incoming email, but he still uses outgoing email, which strikes me as morally inconsistent. Umberto Eco is said (by Knuth) to have no email address at all, which I can’t do, because then I’d have to use the phone. Linda Stone speaks depressingly of our era of “Continuous Partial Attention”; Stone’s right, and thus I harbor a secret master agenda of being one of the few people left on Earth who refuses attention-wasting paraphernalia and thereby become one of the few people who still accomplishes anything new.

But in the past, when I’ve tried to post a stylish and subtly hip disclaimer — not too gruff, not too morally inconsistent, not giving away my phone number, not too revealing of my secret master agenda — I’ve found that the considerate, thoughtful people whom I want to talk to all stop emailing me, and conversely, the people who ask obvious questions because they don’t read documentation don’t read stylish and subtly hip disclaimers either, so they keep emailing me, and as a result I paradoxically enrich for email I don’t want.

Now that HMMER3 is starting to roll out, my email is starting to become even more unmanageable. I’m starting to see a pattern of three main lines of inquiry that I’m going to have to increasingly ignore and feel bad about. In the forlorn hope that someone who doesn’t get a reply from me might check here at the blog rather than just assuming I’m a total jerk, here’s three generic question/answers that cover a lot of email:

How do I do X in HMMER? If you ask me a question that’s already covered in HMMER3’s documentation, I may not reply, in the hope that you realize you can just do your homework. It’s a little awkward to get into a “please read the documentation”, “I did”, “no you didn’t; look at page XX” discussion with a lot of people during the day; partly because I tend to get more testy than I ought to be, partly because I tend to answer in a hurry and make embarrassing mistakes, and partly because it becomes faster to just answer the question rather than have that discussion, but I didn’t have time to answer the question in the first place. Of course, if someone finds something that I haven’t documented well, I always reply, and I always fix the documentation so I don’t have to reply to similar questions in the future. I’m much more likely to reply if someone indicates that they’ve already read the documentation carefully, rather than taking advantage of my easy email accessibility.

How do I do X in this interface to HMMER? If you’re using someone else’s software or web interface to use HMMER, and your problem is in their software not mine, your first point of contact should be the person who developed the interface. That includes commercial software packages that bundle HMMER, and things like BioPerl and other Bio* interfaces. I’m much more likely to reply if a question is directly about HMMER’s own input/output, not something that’s been filtered through someone else’s interface.

How do I do X in this thing that’s called *HMMER* but really isn’t? Programs like MPI-HMMER, GPU-HMMER, LD-HMMER and the like are using the name HMMER without our permission, in annoying disregard of my attempts to get them to use a name that doesn’t confuse people and burden me with a bunch of extra email. Except for the software released by us from, we don’t have anything to do with these other forks or clones, and you again need to contact the people responsible for them.


  1. Sean, have you considered setting up a forum or mailing list so users could answer each others’ questions? MrBayes and PAML are two examples of software I’ve used with reasonably active lists, and I’m guessing that HMMER has a user base big enough to support this approach.



  2. I have, but haven’t gotten as far as doing anything. I’m not a huge fan of mailing lists (see above) but a forum sounds like a good idea. Do you (or does anyone else) have suggestions for setting one up? Looks like XKCD’s forum is running on phpBB, and that looks pretty functional.



  3. Yes, I have to agree with Matt. Set up a Google Group (it takes < 5 minutes), and post the mailing list for that group on the hmmer site instead of your own. To be honest, the couple of times I have emailed you (which you did respond to by the way) I checked to make sure I shouldn't be sending it to some hmmer specific mailing list.

    The biggest benefit is that you might get a few other users actually answering the questions for you. Of course this means that the correspondence on hmmer would be more open and transparent, but I think that would a good thing. Also, it would avoid you getting the same email more than once about such an such a bug.



  4. I’ve read that Google Groups have some pervasive problems, see:

    The comments there mention some alternatives; I think the jQuery team went with Zoho Discussions. Other forums mentioned are phpBB, vBulletin, and FluxBB. Here’s a nifty comparison tool (bordering on overwhelming):

    Maybe such a message board would trade one headache for another (spam moderation, blech). I see the Genetic Software Forum closed up shop in the past year partially for those reasons:

    SEQAnswers is a vBulletin-powered forum that seems active:

    Good luck.



  5. Btw, Sean, How do I compile HMMR3 on an old Altos 586 Xenix machine? 😉

    I support the idea of a forum. SEQanswers, as Matt has suggested, is an excellent place and I have used it extensively to exchange with authors and users. In fact, I’m convinced questions about software should be handled strictly on a forum instead of email – reduces redundacy, is searchable, and users can help each other answer questions.

    I don’t like mailing lists – too annoying to deal with.

    Greetings from Vienna,



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