On the repeat-annotated phylogenetic tree reconstruction problem.

Firas Swidan; Michal Ziv-Ukelson; Ron Y Pinter

doi:10.1089/cmb.2006.13.1397

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On the repeat-annotated phylogenetic tree reconstruction problem.

Firas Swidan·Michal Ziv-Ukelson·Ron Y Pinter

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Abstract

A new problem in phylogenetic inference is presented, based on recent biological findings indicating a strong association between reversals (i.e., inversions) and repeats. These biological findings are formalized here in a new mathematical model, called repeat-annotated phylogenetic trees (RAPT). We show that, under RAPT, the evolutionary process--including both the tree-topology as well as internal node genome orders--is uniquely determined, a property that is of major significance both in theory and in practice. Furthermore, the repeats are employed to provide linear-time algorithms for reconstructing both the genomic orders and the phylogeny, which are NP-hard problems under the classical model of sorting by reversals (SBR).

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Algorithms Computational Biology Genome, Bacterial Models, Biological Phylogeny Recombination, Genetic Repetitive Sequences, Nucleic Acid Journal Article Research Support, Non-U.S. Gov't

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Firas Swidan, Michal Ziv-Ukelson, Ron Y Pinter. 2006. On the repeat-annotated phylogenetic tree reconstruction problem.. https://doi.org/10.1089/cmb.2006.13.1397

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