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    Area of Science:

    • Computational Biology
    • Genomics
    • Phylogenetics

    Background:

    • Sorting circular permutations using reversals is crucial for comparative genomics.
    • The unsigned version of this problem has known polynomial-time solutions.
    • The signed version of this problem remained an open challenge.

    Purpose of the Study:

    • To present the first polynomial-time algorithm for sorting signed circular permutations using super short reversals (length at most 2).
    • To apply the developed methods for inferring bacterial phylogenies.
    • To compare the inferred phylogenies with existing ones.

    Main Methods:

    • Development of a novel polynomial-time algorithm for signed circular permutation sorting.
    • Application of the algorithm to phylogenetic inference for two bacterial groups.
    • Comparative analysis of inferred phylogenies against previous studies.

    Main Results:

    • The first polynomial-time solution for the signed version of the sorting problem is established.
    • Phylogenetic trees were inferred for two bacterial species groups.
    • The results were compared with previously published phylogenetic analyses.

    Conclusions:

    • The presented algorithm provides an efficient solution for a long-standing problem in computational genomics.
    • The study facilitates improved phylogenetic inference using short reversal operations.
    • A web tool is introduced to support further research in rearrangement-based phylogenetics.