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

On word-representability of polyomino triangulations

A graph $G=(V,E)$ is word-representable if there exists a word $w$ over the alphabet $V$ such that letters $x$ and $y$ alternate in $w$ if and only if $(x,y)$ is an edge in $E$. Some graphs are word-representable, others are not. It is known that a graph is word-representable if and only if it accepts a so-called semi-transitive orientation. The main result of this paper is showing that a triangulation of any convex polyomino is word-representable if and only if it is 3-colorable. We demonstrate that this statement is not true for an arbitrary polyomino. We also show that the graph obtained by replacing each $4$-cycle in a polyomino by the complete graph $K_4$ is word-representable. We employ semi-transitive orientations to obtain our results

Proper coloring of geometric hypergraphs

We study whether for a given planar family F there is an m such that any finite set of points can be 3-colored such that any member of F that contains at least m points contains two points with different colors. We conjecture that if F is a family of pseudo-disks, then m = 3 is sufficient. We prove that when F is the family of all homothetic copies of a given convex polygon, then such an m exists. We also study the problem in higher dimensions. © Balázs Keszegh and Dömötör Pálvölgyi

Proper Coloring of Geometric Hypergraphs

We study whether for a given planar family F there is an m such that any finite set of points can be 3-colored so that anymember ofF that contains at leastm points contains two points with different colors. We conjecture that if F is a family of pseudo-disks, then such an m exists. We prove this in the special case when F is the family of all homothetic copies of a given convex polygon. We also study the problem in higher dimensions

Proper Coloring of Geometric Hypergraphs

We study whether for a given planar family F there is an m such that any finite set of points can be 3-colored such that any member of F that contains at least m points contains two points with different colors. We conjecture that if F is a family of pseudo-disks, then m=3 is sufficient. We prove that when F is the family of all homothetic copies of a given convex polygon, then such an m exists. We also study the problem in higher dimensions