Cophenetic metrics for phylogenetic trees, after Sokal and Rohlf

Phylogenetic tree comparison metrics are an important tool in the study of evolution, and hence the definition of such metrics is an interesting problem in phylogenetics. In a paper in Taxon fifty years ago, Sokal and Rohlf proposed to measure quantitatively the difference between a pair of phylogenetic trees by first encoding them by means of their half-matrices of cophenetic values, and then comparing these matrices. This idea has been used several times since then to define dissimilarity measures between phylogenetic trees but, to our knowledge, no proper metric on weighted phylogenetic trees with nested taxa based on this idea has been formally defined and studied yet. Actually, the cophenetic values of pairs of different taxa alone are not enough to single out phylogenetic trees with weighted arcs or nested taxa. In this paper we define a family of cophenetic metrics that compare phylogenetic trees on a same set of taxa by encoding them by means of their vectors of cophenetic values of pairs of taxa and depths of single taxa, and then computing the $L^p$ norm of the difference of the corresponding vectors. Then, we study, either analytically or numerically, some of their basic properties: neighbors, diameter, distribution, and their rank correlation with each other and with other metrics.Comment: The "authors' cut" of a paper published in BMC Bioinformatics 14:3 (2013). 46 page

Dynamic and Multi-functional Labeling Schemes

We investigate labeling schemes supporting adjacency, ancestry, sibling, and connectivity queries in forests. In the course of more than 20 years, the existence of $\log n + O(\log \log)$ labeling schemes supporting each of these functions was proven, with the most recent being ancestry [Fraigniaud and Korman, STOC '10]. Several multi-functional labeling schemes also enjoy lower or upper bounds of $\log n + \Omega(\log \log n)$ or $\log n + O(\log \log n)$ respectively. Notably an upper bound of $\log n + 5\log \log n$ for adjacency+siblings and a lower bound of $\log n + \log \log n$ for each of the functions siblings, ancestry, and connectivity [Alstrup et al., SODA '03]. We improve the constants hidden in the $O$-notation. In particular we show a $\log n + 2\log \log n$ lower bound for connectivity+ancestry and connectivity+siblings, as well as an upper bound of $\log n + 3\log \log n + O(\log \log \log n)$ for connectivity+adjacency+siblings by altering existing methods. In the context of dynamic labeling schemes it is known that ancestry requires $\Omega(n)$ bits [Cohen, et al. PODS '02]. In contrast, we show upper and lower bounds on the label size for adjacency, siblings, and connectivity of $2\log n$ bits, and $3 \log n$ to support all three functions. There exist efficient adjacency labeling schemes for planar, bounded treewidth, bounded arboricity and interval graphs. In a dynamic setting, we show a lower bound of $\Omega(n)$ for each of those families.Comment: 17 pages, 5 figure

A Duality Based 2-Approximation Algorithm for Maximum Agreement Forest

We give a 2-approximation algorithm for the Maximum Agreement Forest problem on two rooted binary trees. This NP-hard problem has been studied extensively in the past two decades, since it can be used to compute the Subtree Prune-and-Regraft (SPR) distance between two phylogenetic trees. Our result improves on the very recent 2.5-approximation algorithm due to Shi, Feng, You and Wang (2015). Our algorithm is the first approximation algorithm for this problem that uses LP duality in its analysis