Related papers: Sorting by Transpositions is Difficult

Sorting a permutation by reversals is a famous problem in genome rearrangements. Since 1997, quite some biological evidence were found that in many genomes the reversed regions are usually flanked by a pair of inverted repeats. This type of…

In the context of the genome rearrangement problem, we analyze two well known models, namely the block transposition and the prefix block transposition models, by exploiting the connection with the notion of permutation pattern. More…

Given a graph where every vertex has exactly one labeled token, how can we most quickly execute a given permutation on the tokens? In (sequential) token swapping, the goal is to use the shortest possible sequence of swaps, each of which…

Genome rearrangement distances are an established method in genome comparison. Works in this area may include various rearrangement operations representing large-scale mutations, gene orientation information, the number of nucleotides in…

Genomic distance between two genomes, i.e., the smallest number of genome rearrangements required to transform one genome into the other, is often used as a measure of evolutionary closeness of the genomes in comparative genomics studies.…

We address the problem of finding the minimum decomposition of a permutation in terms of transpositions with non-uniform cost. For arbitrary non-negative cost functions, we describe polynomial-time, constant-approximation decomposition…

On the string of finite length, a (genomic) transposition is defined as the operation of exchanging two consecutive substrings. The minimum number of transpositions needed to transform one into the other is the transposition distance, that…

Genome assembly, the process of reconstructing a long genetic sequence by aligning and merging short fragments, or reads, is known to be NP-hard, either as a version of the shortest common superstring problem or in a Hamiltonian-cycle…

Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…

We prove a lower and an upper bound on the number of block moves necessary to sort a permutation. We put our results in contrast with existing results on sorting by block transpositions, and raise some open questions.

We study complexity of rearrangement problems in the generalized breakpoint model and settle several open questions. The model was introduced by Tannier et al. (2009) who showed that the median problem is solvable in polynomial time in the…

Perfect sorting by reversals, a problem originating in computational genomics, is the process of sorting a signed permutation to either the identity or to the reversed identity permutation, by a sequence of reversals that do not break any…

A permutation on an alphabet $ \Sigma $, is a sequence where every element in $ \Sigma $ occurs precisely once. Given a permutation $ \pi $= ($\pi_{1} $, $ \pi_{2} $, $ \pi_{3} $,....., $ \pi_{n} $) over the alphabet $ \Sigma $ =$\{ $0, 1,…

We address the problem of finding the minimal number of block interchanges (exchange of two intervals) required to transform a duplicated linear genome into a tandem duplicated linear genome. We provide a formula for the distance as well as…

We initiate the study of sorting permutations using prefix block-interchanges, which exchange any prefix of a permutation with another non-intersecting interval. The goal is to transform a given permutation into the identity permutation…

Sorting a Permutation by Transpositions (SPbT) is an important problem in Bioinformtics. In this paper, we improve the running time of the best known approximation algorithm for SPbT. We use the permutation tree data structure of Feng and…

We prove that computing an evolutionary ordering of a family of sets, i.e. an ordering where each set intersects with --but is not included in-- the union earlier sets, is NP-hard.

We continue the study of Adin, Alon and Roichman [arXiv:2502.14398, 2025] on the number of steps required to sort $n$ labelled points on a circle by transpositions. Imagine that the vertices of a cycle of length $n$ are labelled by the…

In this article, we study the problem of finding the longest common separable pattern between several permutations. We give a polynomial-time algorithm when the number of input permutations is fixed and show that the problem is NP-hard for…

A ternary permutation constraint satisfaction problem (CSP) is specified by a subset Pi of the symmetric group S_3. An instance of such a problem consists of a set of variables V and a set of constraints C, where each constraint is an…