Jakub Kováč, Broňa Brejová, Tomáš Vinař. A New Approach to the Small Phylogeny Problem. Technical Report arXiv:1012.0935, arxiv.org, December 2010.

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In the small phylogeny problem we, are given a phylogenetic tree and gene 
orders of the extant species and our goal is to reconstruct all of the 
ancestral genomes so that the number of evolutionary operations is 
minimized. Algorithms for reconstructing evolutionary history from gene 
orders are usually based on repeatedly computing medians of genomes at 
neighbouring vertices of the tree. We propose a new, more general approach, 
based on an iterative local optimization procedure. In each step, we 
propose candidates for ancestral genomes and choose the best ones by 
dynamic programming. We have implemented our method and used it to 
reconstruct evolutionary history of 16 yeast mtDNAs and 13 Campanulaceae