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The minimum linear arrangement problem on a network consists of finding the minimum sum of edge lengths that can be achieved when the vertices are arranged linearly. Although there are algorithms to solve this problem on trees in polynomial…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
There exists a bijection between one stack sortable permutations --permutations which avoid the pattern 231-- and planar trees. We define an edit distance between permutations which is coherent with the standard edit distance between trees.…
Accessibility percolation is a new type of percolation problem inspired by evolutionary biology. To each vertex of a graph a random number is assigned and a path through the graph is called accessible if all numbers along the path are in…
Phylogenetic networks are a generalization of phylogenetic trees that allow for representation of reticulate evolution. Recently, a space of unrooted phylogenetic networks was introduced, where such a network is a connected graph in which…
We study analytically the late time statistics of the number of particles in a growing tree model introduced by Aldous and Shields. In this model, a cluster grows in continuous time on a binary Cayley tree, starting from the root, by…
We present the distance matrix evolution for different types of networks: exponential, scale-free and classical random ones. Statistical properties of these matrices are discussed as well as topological features of the networks. Numerical…
The selection of the most suitable evolutionary model to analyze the given molecular data is usually left to biologist's choice. In his famous book, J Felsenstein suggested that certain linear equations satisfied by the expected…
Selective inference is considered for testing trees and edges in phylogenetic tree selection from molecular sequences. This improves the previously proposed approximately unbiased test by adjusting the selection bias when testing many trees…
Phylogenetic networks generalize phylogenetic trees in order to model reticulation events. Although the comparison of phylogenetic trees is well studied, and there are multiple ways to do it in an efficient way, the situation is much…
Bayesian phylogenetics is vital for understanding evolutionary dynamics, and requires accurate and efficient approximation of posterior distributions over trees. In this work, we develop a variational Bayesian approach for ultrametric…
The mating of trees approach to Schramm-Loewner evolution (SLE) in the random geometry of Liouville quantum gravity (LQG) has been recently developed by Duplantier-Miller-Sheffield (2014). In this paper we consider the mating of trees…
Frequencies of $k$-mers in sequences are sometimes used as a basis for inferring phylogenetic trees without first obtaining a multiple sequence alignment. We show that a standard approach of using the squared-Euclidean distance between…
Distances on merge trees facilitate visual comparison of collections of scalar fields. Two desirable properties for these distances to exhibit are 1) the ability to discern between scalar fields which other, less complex topological…
Phylogenetic networks are a special type of graph which generalize phylogenetic trees and that are used to model non-treelike evolutionary processes such as recombination and hybridization. In this paper, we consider {\em unrooted}…
An ordered labeled tree is a tree in which the nodes are labeled and the left-to-right order among siblings is relevant. The edit distance between two ordered labeled trees is the minimum cost of changing one tree into the other through a…
The Yule-Harding-Kingman (YHK) model and the proportional to distinguishable arrangements (PDA) model are two binary tree generating models that are widely used in evolutionary biology. Understanding the distributions of clade sizes under…
The marginal likelihood of a model is a key quantity for assessing the evidence provided by the data in support of a model. The marginal likelihood is the normalizing constant for the posterior density, obtained by integrating the product…
We introduce a notion of finite sampling consistency for phylogenetic trees and show that the set of finitely sampling consistent and exchangeable distributions on n leaf phylogenetic trees is a polytope. We use this polytope to show that…
This thesis presents analysis of the properties and run-time of the Rapidly-exploring Random Tree (RRT) algorithm. It is shown that the time for the RRT with stepsize $\epsilon$ to grow close to every point in the $d$-dimensional unit cube…