Giltae Song, Luoxin Zhang, Tomas Vinar, Webb Miller. CAGE: Combinatorial Analysis of Gene-Cluster Evolution. Journal of Computational Biology, 17(9):1227-1232. 2010. Early version appeared in RECOMB-CG 2009.

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Much important evolutionary activity occurs in gene clusters,
where a copy of a gene may be free to acquire new functions. Current
computational methods to extract evolutionary information from sequence
data for such clusters are suboptimal, in part because accurate sequence
data are often lacking in these genomic regions, making existing methods
difficult to apply. We describe a new method for reconstructing the recent
evolutionary history of gene clusters, and evaluate its performance on
both simulated data and actual human gene clusters.