We present two algorithms for calculating the quartet distance between all pairs of trees in a set of binary evolutionary trees on a common set of species. The algorithms exploit common substructure among the trees to speed up the pairwise distance calculations, thus performing significantly better on large sets of trees compared to performing distinct pairwise distance calculations, as we illu...

Abstract. Distance energy is a newly introduced molecular graph-based analog of the total π-electron energy, and it is defined as the sum of the absolute eigenvalues of the molecular distance matrix. For trees and unicyclic graphs, distance energy is equal to the doubled value of the distance spectral radius. In this paper, we introduce a general transformation that increases the distance spect...

Tree structured data often appear in bioinformatics. For example, glycans, RNA secondary structures and phylogenetic trees usually have tree structures. Comparison of trees is one of fundamental tasks in analysis of these data. Various distance measures have been proposed and utilized for comparison of trees, among which extensive studies have been done on tree edit distance. In this paper, we ...

We consider distance labeling schemes for trees: given a tree with n nodes, label the nodes with binary strings such that, given the labels of any two nodes, one can determine, by looking only at the labels, the distance in the tree between the two nodes. A lower bound by Gavoille et al. [Gavoille et al., J. Alg., 2004] and an upper bound by Peleg [Peleg, J. Graph Theory, 2000] establish that l...

Let G be a finite connected graph. If x and y are vertices of G, one may define a distance function d, on G by letting d&x, y) be the minimal length of any path between x and y in G (with d&, x) = 0). Thus, for example, d&x, y) = 1 if and only if {x, y} is an edge of G. Furthermore, we define the distance matrix D(G) for G to be the square matrix with rows and columns indexed by the vertex set ...

We introduce new distance measures for the construction and analysis of phylogenies, focusing on thioredoxin-fold proteins. Our distance measures for tree construction are based on several criteria, including pairwise alignment of only the thioredoxin fold region of each sequence, Hausdorff distance between sequences represented by sets of real vectors derived from per-residue features of the s...

abstract- to study the effect of tree roots on increasing water infiltration in soil and also to determine and assess the coefficients of different infiltration models, some infiltration tests were performed in three tree plantation areas in badjgah, fars province with different soil textures (clay loam for pear plantation, sandy loam for grape plantation, loamy sand for pine trees). in each pl...

Edge shift distance between isomorphism classes of graphs, introduced by M. Johnson, is investigated in the case of trees and compared with other distances .

An L(2, 1, 1)-labeling of a graph G assigns nonnegative integers to the vertices of G in such a way that labels of adjacent vertices differ by at least two, while vertices that are at distance at most three are assigned different labels. The maximum label used is called the span of the labeling, and the aim is to minimize this value. We show that the minimum span of an L(2, 1, 1)-labeling of a ...