Probability models for genome rearrangement and linear invariants for phylogenetic inference
RECOMB '99 Proceedings of the third annual international conference on Computational molecular biology
Hybrid tree reconstruction methods
Journal of Experimental Algorithmics (JEA)
Estimating true evolutionary distances between genomes
STOC '01 Proceedings of the thirty-third annual ACM symposium on Theory of computing
Approximating the Expected Number of Inversions Given the Number of Breakpoints
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Genome Rearrangement Phylogeny Using Weighbor
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
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Evolution operates on whole genomes by operations that change the order and strandedness of genes within the genomes. This type of data presents new opportunities for discoveries about deep evolutionary rearrangement events, provided that sufficiently accurate methods can be developed to reconstruct evolutionary trees in these models [3,11,13,18]. A necessary component of any such method is the ability to accurately estimate the true evolutionary distance between two genomes,which is the number of rearrangement events that took place in the evolutionary history between them. We improve the technique (IEBP) in with a new method, Exact-IEBP, for estimating the true evolutionary distance between two signed genomes. Our simulation study shows Exact-IEBP is a better estimation of true evolutionary distances. Furthermore, Exact-IEBP produces more accurate trees than IEBP when used with the popular distance-based method, neighbor joining [16].