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Great advancements have been achieved in phylogenetic reconstruction from genome rearrangement events but difficult problems still remain. One challenge is to deal with more complex events such as gene insertions and deletions such that we can analyze both gene order and gene content changes in tandem. We propose the concept of prosthetic chromosomes to incorporate these events into the standard double-cut-and-join (DCJ) distance metric widely used for genome scale rearrangement analysis. In this paper, we also introduce our new software package Egchel (Extended Gene Content HEuristic Layer) which implements this prosthetic chromosome model. Egchel can modify unequal content gene order data sets such that they are able to be analyzed by existing phylogenetic tree builders specifically designed to work with equal content gene order data sets. When compared to existing pairwise analysis of unequal content data sets, Egchel uses a global approach, produces substantially more accurate phylogenetic trees, and is significantly more likely to generate the best available tree.