This invention provides methods of obtaining novel polynucleotides and encoded polypeptides by use of non-stochastic methods of 
directed evolution (DirectEvolution(TM)). These methods include non-stochastic 
polynucleotide site-saturation 
mutagenesis (
Gene Site Saturation 
Mutagenesis(TM)) and non-stochastic 
polynucleotide reassembly (GeneReassembly(TM)). Through use of the claimed methods, genetic vaccines, enzymes, and other desirable molecules can be evolved towards desirable properties. For example, vaccine vectors can be obtained that exhibit increased 
efficacy for use as genetic vaccines. Vectors obtained by using the methods can have, for example, enhanced 
antigen expression, increased uptake into a 
cell, increased stability in a 
cell, ability to tailor an immune response, and the like. This invention provides methods of obtaining novel enzymes that have optimized physical & / or biological properties. Furthermore, this invention provides methods of obtaining a variety of novel biologically active molecules, in the fields of 
antibiotics, pharmacotherapeutics, and transgenic traits.