Abstract
Genome rearrangements are evolutionary events that shuffle genomic architectures. Usually the rearrangement distance between two genomes is estimated as the minimal number of rearrangements needed to transform one genome into another, which is usually referred to as the parsimony assumption.
Since in reality the parsimony assumption may or may not hold, the question arises of estimating the true evolutionary distance (i.e., the actual number of genome rearrangements between the genomes of two species). While several methods for solving this problem have been developed, all of them have their own disadvantages. In the current paper we consider a very general model and provide a flexible estimator as well as the limits of applicability for the most popular estimation methods, such as the maximum parsimony method.
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Notes
- 1.
In the breakpoint graph constructed on synteny blocks of two genomes, there are no trivial cycles since no adjacency is shared by both genomes. However, the breakpoint graph constructed on orthologous genes or multi-genome synteny blocks may contain trivial cycles.
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Acknowledgments
The authors thank Artem Vasilyev and Pavel Avdeyev for fruitful discussions and the anonymous reviewers for valuable comments.
The work of NA was financially supported by the Government of the Russian Federation through the ITMO Fellowship and Professorship Program. The work of AZ was financially supported by the Government of the Russian Federation (Grant 08-08).
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Zabelkin, A., Alexeev, N. (2018). Estimation of the True Evolutionary Distance Under the INFER Model. In: Blanchette, M., Ouangraoua, A. (eds) Comparative Genomics. RECOMB-CG 2018. Lecture Notes in Computer Science(), vol 11183. Springer, Cham. https://doi.org/10.1007/978-3-030-00834-5_4
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