I worked with Bob some ~20 years ago at Berkeley. he showed up one day to check out the seminars and see if he could "help out" after having sold his database company to Intel. he said he'd been trained as a physics guy in the 80s but there were no real jobs so he started a software company instead. He joined my advisor's group (it helped a lot, because at the time most journals wouldn't publish a paper submitted from a home address).

He proceeded to completely understand hidden markov models and protein sequence alignment and was immediately hacking improvements to HMMER. However, Sean Eddy couldn't understand his optimizations (Sean has to know how HMMER works at all times) and so Bob went off and made his own tools like MUSCLE.

One of the reasons he can do this is, well, he's a programmer/math genius, and the other reason is that HMMs and protein alignments are a fairly well understood and programmable thing these days.

Still blows me away we train up all these people to be scientists when there are no jobs for them in that role.

I don't work in this space anymore, but just want to say kseq (and the rest of klib) is such an awesome time saver. Thank you.