Yu Zhang, Giltae Song, Tomas Vinar, Eric D. Green, Adam Siepel, Webb Miller. Evolutionary History Reconstruction for Mammalian Complex Gene Clusters. Journal of Computational Biology, 16(8):1051-1070. 2009. Early version appeared in RECOMB 2008.

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Clusters of genes that evolved from single progenitors via repeated 
segmental duplications present significant challenges to the generation of 
a truly complete human genome sequence. Such clusters can confound both 
accurate sequence assembly and downstream computational analysis, yet they 
represent a hotbed of functional innovation, making them of extreme 
interest. We have developed an algorithm for reconstructing the 
evolutionary history of gene clusters using only human genomic sequence 
data, which allows the tempo of largescale evolutionary events in human 
gene clusters to be estimated. We further propose an extension of the 
method to simultaneously reconstructing the evolutionary histories of 
orthologous gene clusters in multiple primates, which will facilitate 
primate comparative sequencing studies that aim to reconstruct their 
evolutionary history more fully.