Advances in phylogeny reconstruction from gene order and content data
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Updated: Aug 18, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Bernard M E Moret1, Tandy Warnow
1Department of Computer Sciences, University of New Mexico, Albuquerque, New Mexico 87131, USA.
Abstract:
Genomes can be viewed in terms of their gene content and the order in which the genes appear along each chromosome. Evolutionary events that affect the gene order or content are "rare genomic events" (rarer than events that affect the composition of the nucleotide sequences) and have been advocated by systematists for inferring deep evolutionary histories. This chapter surveys recent developments in the reconstruction of phylogenies from gene order and content, focusing on their performance under various stochastic models of evolution. Because such methods are quite restricted in the type of data they can analyze, we also present research aimed at handling the full range of whole-genome data.
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