1. A method of identifying a set of oligonucleotides for use in an in vitro recombination procedure, the method comprising: (a) receiving data identifying sequences of two or more parental polypeptides or parental nucleic acids that encode the polypeptides; (b) selecting one or more cross-over sites on the sequences based on structural information about the parental polypeptides or polypeptides encoded by the parental nucleic acids; thereby defining one or more recombinant polypeptides or recombinant nucleic acids that result from cross-overs between the parental polypeptides or nucleic acids at the one or more cross-over sites; (c) selecting at least one of the recombinant polypeptides or recombinant nucleic acids; (d) identifying one or more oligonucleotides for in vitro recombination by choosing at least one portion of at least one of the recombinant polypeptides or recombinant nucleic acids selected in (c) which at least one portion identifies the one or more oligonucleotides for in vitro recombination; and (e) outputting the identities of the one or more oligonucleotides for in vitro recombination, wherein each of operations (a) through (e) is performed via a suitably programmed computer system.