We provide several sets of reference sequences generated based on the 1000 Genomes Project data. In order to save disk space and improve the efficiency of file reading, the reference sequence file for SeqSIMLA is a binary zip file. Therefore, if you would like to use your own reference sequence files, the files need to be converted to the binary format first. In the SeqSIMLA package, we provide a tool called "convert" to do the job. In the bin directory, you can find a binary executable file convert. If you would like to compile from the source, enter the convert directory and type make to generate a binary executable file. There are three steps to generate the reference sequence files for SeqSIMLA.