This was from a few months ago, published in the journal Nucleic Acids Research:
So how do you pronounce 'FunFHMMer'? I can imagine several possibilities:
Reading the manuscript suggests that 'FunF' stems from 'FunFam(s)' which in turn is derived from 'functional families'. This would suggest that options 1 or 3 above might be the correct way to pronounce this software's name.
The fully expanded description of this web server's name becomes a bit of a mouthful:
Class Architecture Topology Homologous Superfamily Functional Families Hidden Markov Model (maker?)