The quantitative study of evolution based on comparative map data is dependent on the definition and identification of conserved segments remaining after interchromosomal exchanges such as reciprocal translocation. Because of experimental error and, more important, extensive local intrachromosomal rearrangement, it is difficult to reconstruct the configuration of conserved segments produced by interchromosomal exchanges. We present a formula to evaluate possible conserved segments and an algorithm which seeks the partition of the genome into segments optimal under this evaluation. Application is made to the human-mouse comparison.