4 citations · 9 across the 11 of their papers we have counts for
13 papers
Statistical learning with phylogenetic network invariants
Travis Barton, Elizabeth Gross, Colby Long +1
Phylogenetic networks provide a means of describing the evolutionary history of sets of species believed to have undergone hybridization or gene flow during their evolution. The mu…
Constructing Semi-Directed Level-1 Phylogenetic Networks from Quarnets
Sophia Huebler, Rachel Morris, Joseph Rusinko
Semi-directed networks provide a graphical structure for describing the evolutionary history of organisms in the presence of hybridization. We introduce two algorithms for reconstr…
Phylogenetic Networks
Elizabeth Gross, Colby Long, Joseph Rusinko
Phylogenetics is the study of the evolutionary relationships between organisms. One of the main challenges in the field is to take biological data for a group of organisms and to i…
Phylogenetic Derivative: A Tool for Assessing Local Tree Reconstruction in the Presence of Recombination
Jacqueline Kane, Joseph Rusinko, Katherine Thompson
Recently, much attention has been given to understanding recombination events along a chromosome in a variety of field. For instance, many population genetics problems are limited…
Species tree estimation using Neighbor Joining
Joseph Rusinko, Matthew McPartlon
Recent theoretical work has demonstrated that Neighbor Joining applied to concatenated DNA sequences is a statistically consistent method of species tree reconstruction. This brief…
Modeling the distribution of distance data in Euclidean space
Ruth Davidson, Joseph Rusinko, Zoe Vernon +1
Phylogenetic inference-the derivation of a hypothesis for the common evolutionary history of a group of species- is an active area of research at the intersection of biology, compu…
Efficient Quartet Representations of Trees and Applications to Supertree and Summary Methods
Ruth Davidson, MaLyn Lawhorn, Joseph Rusinko +1
Quartet trees displayed by larger phylogenetic trees have long been used as inputs for species tree and supertree reconstruction. Computational constraints prevent the use of all d…
H-Representation of the Kimura-3 Polytope
Marie Mauhar, Joseph Rusinko, Zoe Vernon
Given a group-based Markov model on a tree, one can compute the vertex representation of a polytope which describes the associated toric variety. The half-space representation, how…
Combinatorics of k-Interval Cospeciation for Cophylogeny
Jane Ivy Coons, Joseph Rusinko
We show that the cophylogenetic distance, k-interval cospeciation, is distinct from other metrics and accounts for global congruence between locally incongruent trees. The growth o…
Combinatorics of Linked Systems of Quartet Trees
Emili Moan, Joseph Rusinko
We apply classical quartet techniques to the problem of phylogenetic decisiveness and find a value such that all collections of at least quartets are decisive. Moreover, we…
Invariant Based Quartet Puzzling
Joe Rusinko, Brian Hipp
Traditional Quartet Puzzling algorithms use maximum likelihood methods to reconstruct quartet trees, and a puzzling algorithm to combine these quartets into a tree for the full col…
Commutation classes of double wiring diagrams
Patrick Dukes, Joe Rusinko
We describe a new method for computing the graph of commutation classes of double wiring diagrams. Using these methods we compute the graph for five strings or less which allows us…
Equivalence of Mirror Families Constructed from Toric Degenerations of Flag Varieties
Joe Rusinko
Batyrev (et. al.) constructed a family of Calabi-Yau varieties using small toric degenerations of the full flag variety G/B. They conjecture this family to be mirror to generic ant…