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Conference Papers Year : 2012

Preserving Inversion Phylogeny Reconstruction

Abstract

Tractability results are rare in the comparison of gene orders for more than two genomes. Here we present a linear-time algorithm for the small parsimony problem (inferring ancestral genomes given a phylogeny on an arbitrary number of genomes) in the case gene orders are permutations, that evolve by inversions not breaking common gene intervals, and these intervals are organised in a linear structure. We present two examples where this allows to reconstruct the ancestral gene orders in phylogenies of several γ-Proteobacteria species and Burkholderia strains, respectively.We prove in addition that the large parsimony problem (where the phylogeny is output) remains NP-complete.
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Dates and versions

hal-00733188 , version 1 (18-09-2012)

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Matthias Bernt, Kun-Mao Chao, Jyun-Wei Kao, Martin Middendorf, Eric Tannier. Preserving Inversion Phylogeny Reconstruction. WABI 2012 - 12th International Workshop on Algorithms in Bioinformatics, Sep 2012, Ljubljana, Slovenia. pp.1-13, ⟨10.1007/978-3-642-33122-0_1⟩. ⟨hal-00733188⟩
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