Algorithms for Visualizing Phylogenetic Networks

We study the problem of visualizing phylogenetic networks, which are extensions of the Tree of Life in biology. We use a space filling visualization method, called DAGmaps, in order to obtain clear visualizations using limited space. In this paper, we restrict our attention to galled trees and galled networks and present linear time algorithms for visualizing them as DAGmaps.Comment: Appears in the Proceedings of the 24th International Symposium on Graph Drawing and Network Visualization (GD 2016

Randomized Search of Graphs in Log Space and Probabilistic Computation

Reingold has shown that L = SL, that s-t connectivity in a poly-mixing digraph is complete for promise-RL, and that s-t connectivity for a poly-mixing out-regular digraph with known stationary distribution is in L. Several properties that bound the mixing times of random walks on digraphs have been identified, including the digraph conductance and the digraph spectral expansion. However, rapidly mixing digraphs can still have exponential cover time, thus it is important to specifically identify structural properties of digraphs that effect cover times. We examine the complexity of random walks on a basic parameterized family of unbalanced digraphs called Strong Chains (which model weakly symmetric logspace computations), and a special family of Strong Chains called Harps. We show that the worst case hitting times of Strong Chain families vary smoothly with the number of asymmetric vertices and identify the necessary condition for non-polynomial cover time. This analysis also yields bounds on the cover times of general digraphs. Next we relate random walks on graphs to the random walks that arise in Monte Carlo methods applied to optimization problems. We introduce the notion of the asymmetric states of Markov chains and use this definition to obtain some results about Markov chains. We also obtain some results on the mixing times for Markov Chain Monte Carlo Methods. Finally, we consider the question of whether a single long random walk or many short walks is a better strategy for exploration. These are walks which reset to the start after a fixed number of steps. We exhibit digraph families for which a few short walks are far superior to a single long walk. We introduce an iterative deepening random search. We use this strategy estimate the cover time for poly-mixing subgraphs. Finally we discuss complexity theoretic implications and future work

Gene Family Histories: Theory and Algorithms

Detailed gene family histories and reconciliations with species trees are a prerequisite for studying associations between genetic and phenotypic innovations. Even though the true evolutionary scenarios are usually unknown, they impose certain constraints on the mathematical structure of data obtained from simple yes/no questions in pairwise comparisons of gene sequences. Recent advances in this field have led to the development of methods for reconstructing (aspects of) the scenarios on the basis of such relation data, which can most naturally be represented by graphs on the set of considered genes. We provide here novel characterizations of best match graphs (BMGs) which capture the notion of (reciprocal) best hits based on sequence similarities. BMGs provide the basis for the detection of orthologous genes (genes that diverged after a speciation event). There are two main sources of error in pipelines for orthology inference based on BMGs. Firstly, measurement errors in the estimation of best matches from sequence similarity in general lead to violations of the characteristic properties of BMGs. The second issue concerns the reconstruction of the orthology relation from a BMG. We show how to correct estimated BMG to mathematically valid ones and how much information about orthologs is contained in BMGs. We then discuss implicit methods for horizontal gene transfer (HGT) inference that focus on pairs of genes that have diverged only after the divergence of the two species in which the genes reside. This situation defines the edge set of an undirected graph, the later-divergence-time (LDT) graph. We explore the mathematical structure of LDT graphs and show how much information about all HGT events is contained in such LDT graphs