Related papers: Sorting by Transpositions is Difficult
We study the connections between sorting and the binary search tree (BST) model, with an aim towards showing that the fields are connected more deeply than is currently appreciated. While any BST can be used to sort by inserting the keys…
We consider the following problem: from a given set of gene families trees on a set of genomes, find a first speciation, that splits these genomes into two subsets, that minimizes the number of gene duplications that happened before this…
A mathematical algorithm to describe DNA or RNA sequences of $N$ nucleotides by a string of $2N$ integers numbers is presented in the framework of the so called crystal basis model of the genetic code. The description allows to define a not…
Permutation tests are amongst the most commonly used statistical tools in modern genomic research, a process by which p-values are attached to a test statistic by randomly permuting the sample or gene labels. Yet permutation p-values…
We describe a new method for finding patterns in permutations that produce a given pattern after the permutation has been passed once through a stack. We use this method to describe West-3-stack-sortable permutations, that is, permutations…
Motivation The Burrows-Wheeler transform (BWT) is the foundation of many algorithms for compression and indexing of text data, but the cost of computing the BWT of very large string collections has prevented these techniques from being…
We say that a permutation $\pi$ is a Motzkin permutation if it avoids 132 and there do not exist $a<b$ such that $\pi_a<\pi_b<\pi_{b+1}$. We study the distribution of several statistics in Motzkin permutations, including the length of the…
The variation in genome arrangements among bacterial taxa is largely due to the process of inversion. Recent studies indicate that not all inversions are equally probable, suggesting, for instance, that shorter inversions are more frequent…
We show that the problem of computing the distance of a given permutation from a subgroup $H$ of $S_n$ is in general NP-complete, even under the restriction that $H$ is elementary Abelian of exponent 2. The problem is shown to be…
The problem of genealogy of permutations has been solved partially by Stefan (odd order) and Acosta-Hum\'anez \& Bernhardt (power of two). It is well known that Sharkovskii's theorem shows the relationship between the cardinal of the set of…
We explore various techniques to compress a permutation $\pi$ over n integers, taking advantage of ordered subsequences in $\pi$, while supporting its application $\pi$(i) and the application of its inverse $\pi^{-1}(i)$ in small time. Our…
Network topologies can be non-trivial, due to the complex underlying behaviors that form them. While past research has shown that some processes on networks may be characterized by low-order statistics describing nodes and their neighbors,…
Define a permutation to be any sequence of distinct positive integers. Given two permutations p and s on disjoint underlying sets, we denote by p sh s the set of shuffles of p and s (the set of all permutations obtained by interleaving the…
A notation system was previously presented which can notate any rational frequency in free Just Intonation. Transposition of music is carried out by multiplying each member of a set of frequencies by a single frequency. Transposition of JI…
Permutation patterns and pattern avoidance are central, well-studied concepts in combinatorics and computer science. Given two permutations $\tau$ and $\pi$, the pattern matching problem (PPM) asks whether $\tau$ contains $\pi$. This…
In a genetic algorithm, fluctuations of the entropy of a genome over time are interpreted as fluctuations of the information that the genome's organism is storing about its environment, being this reflected in more complex organisms. The…
Genetic Programming (GP) has found various applications. Understanding this type of algorithm from a theoretical point of view is a challenging task. The first results on the computational complexity of GP have been obtained for problems…
There exists a bijection between one stack sortable permutations --permutations which avoid the pattern 231-- and planar trees. We define an edit distance between permutations which is coherent with the standard edit distance between trees.…
The complexity class NP of decision problems that can be solved nondeterministically in polynomial time is of great theoretical and practical importance where the notion of polynomial-time reductions between NP-problems is a key concept for…
In this paper, we introduce plane permutations, i.e. pairs $\mathfrak{p}=(s,\pi)$ where $s$ is an $n$-cycle and $\pi$ is an arbitrary permutation, represented as a two-row array. Accordingly a plane permutation gives rise to three distinct…