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Preserving Inversion Phylogeny Reconstruction

Matthias Bernt 1 Kun-Mao Chao 2 Jyun-Wei Kao 2 Martin Middendorf 1 Eric Tannier 3, 4
1 Institut für Informatik [Leipzig]
2 Institute of CSIE - Institute of Computer Science and Information Engineering [Taiwan]
3 BPGE - Bioinformatique, phylogénie et génomique évolutive
PEGASE - Département PEGASE [LBBE]
4 BEAGLE - Artificial Evolution and Computational Biology
LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558, Inria Grenoble - Rhône-Alpes, LIRIS - Laboratoire d'InfoRmatique en Image et Systèmes d'information
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.
Keywords : Signed permutation Common interval Binary Character Gene order Character state
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Conference papers
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https://hal.archives-ouvertes.fr/hal-00733188
Contributor : Eric Tannier <>
Submitted on : Tuesday, September 18, 2012 - 10:52:53 AM
Last modification on : Tuesday, July 20, 2021 - 5:20:05 PM

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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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