Giltae Song, Louxin Zhang, Tomas Vinar, Webb Miller. Inferring the Recent Duplication History of a Gene Cluster. In F. D. Ciccarelli, I. Miklos, ed., Comparative Genomics, International Workshop (RECOMB-CG), 5817 volume of Lecture Notes in Bioinformatics, pp. 111-125, Budapest, September 2009. Springer.

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Much important evolutionary activity occurs in gene clusters, where a copy 
of a gene may be free to evolve new functions. Computational methods to 
extract evolutionary information from sequence data for such clusters are 
currently imperfect, in part because accurate sequence data are often 
lacking in these genomic regions, making the existing methods difficult to 
apply. We describe a new method for reconstructing the recent evolutionary 
history of gene clusters. The method's performance is evaluated on simulated data and on actual human gene clusters.