Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots

Although taxonomy is often used informally to evaluate the results of phylogenetic inference and find the root of phylogenetic trees, algorithmic methods to do so are lacking. In this paper we formalize these procedures and develop algorithms to solve the relevant problems. In particular, we introduce a new algorithm that solves a "subcoloring" problem for expressing the difference between the taxonomy and phylogeny at a given rank. This algorithm improves upon the current best algorithm in terms of asymptotic complexity for the parameter regime of interest; we also describe a branch-and-bound algorithm that saves orders of magnitude in computation on real data sets. We also develop a formalism and an algorithm for rooting phylogenetic trees according to a taxonomy. All of these algorithms are implemented in freely-available software.Comment: Version submitted to Algorithms for Molecular Biology. A number of fixes from previous versio

Product Dimension of Forests and Bounded Treewidth Graphs

The product dimension of a graph G is defined as the minimum natural number l such that G is an induced subgraph of a direct product of l complete graphs. In this paper we study the product dimension of forests, bounded treewidth graphs and k-degenerate graphs. We show that every forest on n vertices has a product dimension at most 1.441logn+3. This improves the best known upper bound of 3logn for the same due to Poljak and Pultr. The technique used in arriving at the above bound is extended and combined with a result on existence of orthogonal Latin squares to show that every graph on n vertices with a treewidth at most t has a product dimension at most (t+2)(logn+1). We also show that every k-degenerate graph on n vertices has a product dimension at most \ceil{8.317klogn}+1. This improves the upper bound of 32klogn for the same by Eaton and Rodl.Comment: 12 pages, 3 figure

Constrained Ramsey Numbers

For two graphs S and T, the constrained Ramsey number f(S, T) is the minimum n such that every edge coloring of the complete graph on n vertices, with any number of colors, has a monochromatic subgraph isomorphic to S or a rainbow (all edges differently colored) subgraph isomorphic to T. The Erdos-Rado Canonical Ramsey Theorem implies that f(S, T) exists if and only if S is a star or T is acyclic, and much work has been done to determine the rate of growth of f(S, T) for various types of parameters. When S and T are both trees having s and t edges respectively, Jamison, Jiang, and Ling showed that f(S, T) <= O(st^2) and conjectured that it is always at most O(st). They also mentioned that one of the most interesting open special cases is when T is a path. In this work, we study this case and show that f(S, P_t) = O(st log t), which differs only by a logarithmic factor from the conjecture. This substantially improves the previous bounds for most values of s and t.Comment: 12 pages; minor revision