Related papers: An Algorithm to Enumerate Grid Signed Permutation …
Sorting by reversals is an important problem in inferring the evolutionary relationship between two genomes. The problem of sorting unsigned permutation has been proven to be NP-hard. The best guaranteed error bounded is the 3/2-…
In this paper, we reveal an intriguing relationship between two seemingly unrelated notions: letter graphs and geometric grid classes of permutations. An important property common for both of them is well-quasi-orderability, implying, in a…
We describe an algorithm, implemented in Python, which can enumerate any permutation class with polynomial enumeration from a structural description of the class. In particular, this allows us to find formulas for the number of permutations…
A geometric grid class consists of those permutations that can be drawn on a specified set of line segments of slope \pm1 arranged in a rectangular pattern governed by a matrix. Using a mixture of geometric and language theoretic methods,…
We introduce an algorithm that conjectures the structure of a permutation class in the form of a disjoint cover of "rules"; similar to generalized grid classes. The cover is usually easily verified by a human and translated into an…
The simple permutations in two permutation classes --- the 321-avoiding permutations and the skew-merged permutations --- are enumerated using a uniform method. In both cases, these enumerations were known implicitly, by working backwards…
We introduce and characterise grid classes, which are natural generalisations of other well-studied permutation classes. This characterisation allows us to give a new, short proof of the Fibonacci dichotomy: the number of permutations of…
A grid class consists of permutations whose pictorial depiction can be partitioned into increasing and decreasing parts as determined by a given matrix. In this paper, we introduce a method for enumerating cyclic permutations in vector grid…
We study aspects of the enumeration of permutation classes, sets of permutations closed downwards under the subpermutation order. First, we consider monotone grid classes of permutations. We present procedures for calculating the generating…
Arc permutations, which were originally introduced in the study of triangulations and characters, have recently been shown to have interesting combinatorial properties. The first part of this paper continues their study by providing signed…
We exhibit a procedure to asymptotically enumerate monotone grid classes of permutations. This is then applied to compute the asymptotic number of permutations in any connected one-corner class. Our strategy consists of enumerating the…
A sequence of reversals that takes a signed permutation to the identity is perfect if at no step a common interval is broken. Determining a parsimonious perfect sequence of reversals that sorts a signed permutation is NP-hard. Here we show…
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…
Computing the reversal distances of signed permutations is an important topic in Bioinformatics. Recently, a new lower bound for the reversal distance was obtained via the plane permutation framework. This lower bound appears different from…
We obtain an upper and lower bound for the number of reduced words for a permutation in terms of the number of braid classes and the number of commutation classes of the permutation. We classify the permutations that achieve each of these…
In this dissertation, we explore the structure of inversion graphs of permutations--a class of graphs that naturally arises by representing each permutation as a graph, where vertices correspond to entries and edges encode inversions.…
A pattern class is a set of permutations closed under the formation of subpermutations. Such classes can be characterised as those permutations not involving a particular set of forbidden permutations. A simple collection of necessary and…
In this paper we present a simple framework to study various distance problems of permutations, including the transposition and block-interchange distance of permutations as well as the reversal distance of signed permutations. These…
In the context of the genome rearrangement problem, we analyze two well known models, namely the reversal and the prefix reversal models, by exploiting the connection with the notion of permutation pattern. More specifically, for any $k$,…
The periodic (ordinal) patterns of a map are the permutations realized by the relative order of the points in its periodic orbits. We give a combinatorial characterization of the periodic patterns of an arbitrary signed shift, in terms of…