We were able to integrate missing values into the transitivity clustering process. From a user perspective, only the creation of the cost matrices changed. Here, we present our new tool for the creation of cost matrices, the CostMatrixCreator. This tool supports the user to efficiently create cost matrices, especially for large projects. This Creator supports the user to generate cost matrices by only providing your protein sequences in FASTA format and a link to your BLAST executables. The support for missing values drastically reduces the BLAST running time while keeping the cluster quality at a high level. Afterwards, the resulting cost matrices can be fed to the normal TransClust tool, or can upload to our convenient web-interface. For further information, please refer to the documentation for the stand alone executable or for our online service.