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

First-Fit coloring of Cartesian product graphs and its defining sets

Let the vertices of a Cartesian product graph $G\Box H$ be ordered by an ordering $\sigma$. By the First-Fit coloring of $(G\Box H, \sigma)$ we mean the vertex coloring procedure which scans the vertices according to the ordering $\sigma$ and for each vertex assigns the smallest available color. Let $FF(G\Box H,\sigma)$ be the number of colors used in this coloring. By introducing the concept of descent we obtain a sufficient condition to determine whether $FF(G\Box H,\sigma)=FF(G\Box H,\tau)$, where $\sigma$ and $\tau$ are arbitrary orders. We study and obtain some bounds for $FF(G\Box H,\sigma)$, where $\sigma$ is any quasi-lexicographic ordering. The First-Fit coloring of $(G\Box H, \sigma)$ does not always yield an optimum coloring. A greedy defining set of $(G\Box H, \sigma)$ is a subset $S$ of vertices in the graph together with a suitable pre-coloring of $S$ such that by fixing the colors of $S$ the First-Fit coloring of $(G\Box H, \sigma)$ yields an optimum coloring. We show that the First-Fit coloring and greedy defining sets of $G\Box H$ with respect to any quasi-lexicographic ordering (including the known lexicographic order) are all the same. We obtain upper and lower bounds for the smallest cardinality of a greedy defining set in $G\Box H$, including some extremal results for Latin squares.Comment: Accepted for publication in Contributions to Discrete Mathematic

Reconfiguration in bounded bandwidth and treedepth

We show that several reconfiguration problems known to be PSPACE-complete remain so even when limited to graphs of bounded bandwidth. The essential step is noticing the similarity to very limited string rewriting systems, whose ability to directly simulate Turing Machines is classically known. This resolves a question posed open in [Bonsma P., 2012]. On the other hand, we show that a large class of reconfiguration problems becomes tractable on graphs of bounded treedepth, and that this result is in some sense tight.Comment: 14 page

Semi-algebraic colorings of complete graphs

We consider $m$-colorings of the edges of a complete graph, where each color class is defined semi-algebraically with bounded complexity. The case $m = 2$ was first studied by Alon et al., who applied this framework to obtain surprisingly strong Ramsey-type results for intersection graphs of geometric objects and for other graphs arising in computational geometry. Considering larger values of $m$ is relevant, e.g., to problems concerning the number of distinct distances determined by a point set. For $p\ge 3$ and $m\ge 2$, the classical Ramsey number $R(p;m)$ is the smallest positive integer $n$ such that any $m$-coloring of the edges of $K_n$, the complete graph on $n$ vertices, contains a monochromatic $K_p$. It is a longstanding open problem that goes back to Schur (1916) to decide whether $R(p;m)=2^{O(m)}$, for a fixed $p$. We prove that this is true if each color class is defined semi-algebraically with bounded complexity. The order of magnitude of this bound is tight. Our proof is based on the Cutting Lemma of Chazelle {\em et al.}, and on a Szemer\'edi-type regularity lemma for multicolored semi-algebraic graphs, which is of independent interest. The same technique is used to address the semi-algebraic variant of a more general Ramsey-type problem of Erd\H{o}s and Shelah