Generating high-quality mutant libraries in which each amino acid is equally targeted and substituted in a chemically diverse manner is crucial to obtain improved variants in small mutant libraries. The sequence saturation mutagenesis method (SeSaM-Tv(+) ) offers the opportunity to generate such high-quality mutant libraries by introducing consecutive mutations and by enriching transversions. In this study, automated gel electrophoresis, real-time quantitative PCR, and a phosphorimager quantification system were developed and employed to optimize each step of previously reported SeSaM-Tv(+) method. Advancements of the SeSaM-Tv(+) protocol and the use of a novel DNA polymerase quadrupled the number of transversions, by doubling the fraction of consecutive mutations (from 16.7 to 37.1 %). About 33 % of all amino acid substitutions observed in a model library are rarely introduced by epPCR methods, and around 10 % of all clones carried amino acid substitutions that are unobtainable by epPCR.