Hammering Down on HMMer

Things are heating up in the blogosphere between developers of HMMer, the freely available popular sequence analysis tool originally written by Sean Eddy of Janelia Farms. Scalability has a post pointing out some issues related to a trademark for HMMer granted to Eddy back in early April. Currently, there several open source "flavors" or "forked off" versions of HMMer, such as GPU-HMMer and mpiHMMer, that may have to be renamed or no longer distributed due to the stipulations in the trademark. While Eddy argues that the trademark will help to cut down on confusion in the user community due to these other versions, Scalability says that the other versions are merely just derivatives of HMMer, allowable under GPL rules, and that restricting use of the name will only frustrate HMMer developers and hurt the cause in the end.