TruEst: a better estimator of evolutionary distance under the INFER model.

Genome rearrangements are evolutionary events that shuffle genomic architectures. The number of genome rearrangements that happened between two genomes is often used as the evolutionary distance between these species. This number is often estimated as the minimum number of genome rearrangements required to transform one genome into another which are only reliable for closely-related genomes. These estimations often underestimate the evolutionary distance for genomes that have substantially evolved from each other, and advanced statistical methods can be used to improve accuracy. Several statistical estimators have been developed, under various evolutionary models, of which the most complete one, INFER, takes into account different degrees of genome fragility. We present TruEst-an efficient tool that estimates the evolutionary distance between the genomes under the INFER model of genome rearrangements. We apply our method to both simulated and real data. It shows high accuracy on the simulated data. On the real datasets of mammal genomes the method found several pairs of genomes for which the estimated distances are in high consistency with the previous ancestral reconstruction studies.