{\Gamma}-species and the enumeration of k-trees

We study the class of graphs known as k-trees through the lens of Joyal's theory of combinatorial species (and an equivariant extension known as '$\Gamma$-species' which incorporates data about 'structural' group actions). This culminates in a system of recursive functional equations giving the generating function for unlabeled k-trees which allows for fast, efficient computation of their numbers. Enumerations up to k = 10 and n = 30 (for a k-tree with (n+k-1) vertices) are included in tables, and Sage code for the general computation is included in an appendix.Comment: 26 pages; includes Python cod

Geometric combinatorics and computational molecular biology: branching polytopes for RNA sequences

Questions in computational molecular biology generate various discrete optimization problems, such as DNA sequence alignment and RNA secondary structure prediction. However, the optimal solutions are fundamentally dependent on the parameters used in the objective functions. The goal of a parametric analysis is to elucidate such dependencies, especially as they pertain to the accuracy and robustness of the optimal solutions. Techniques from geometric combinatorics, including polytopes and their normal fans, have been used previously to give parametric analyses of simple models for DNA sequence alignment and RNA branching configurations. Here, we present a new computational framework, and proof-of-principle results, which give the first complete parametric analysis of the branching portion of the nearest neighbor thermodynamic model for secondary structure prediction for real RNA sequences.Comment: 17 pages, 8 figure

Counting unlabeled k-trees

Abstract We count unlabeled k-trees by properly coloring them in k + 1 colors and then counting orbits of these colorings under the action of the symmetric group on the colors