44 citations · 52 across the 14 of their papers we have counts for
8 papers · 1 filter
Testing the Agreement of Trees with Internal Labels
David Fernández-Baca, Lei Liu
The input to the agreement problem is a collection of phylogenetic trees, called input trees, over partially overlapping sets of taxa. The question…
Fast Compatibility Testing for Phylogenies with Nested Taxa
Yun Deng, David Fernández-Baca
Semi-labeled trees are phylogenies whose internal nodes may be labeled by higher-order taxa. Thus, a leaf labeled Mus musculus could nest within a subtree whose root node is labele…
Fast Compatibility Testing for Rooted Phylogenetic Trees
Yun Deng, David Fernández-Baca
We consider the following basic problem in phylogenetic tree construction. Let be a collection of rooted phylogenetic trees over various subset…
Constructing and Employing Tree Alignment Graphs for Phylogenetic Synthesis
Ruchi Chaudhary, David Fernandez-Baca, J. Gordon Burleigh
Tree alignment graphs (TAGs) provide an intuitive data structure for storing phylogenetic trees that exhibits the relationships of the individual input trees and can potentially ac…
Inferring Species Trees from Incongruent Multi-Copy Gene Trees Using the Robinson-Foulds Distance
Ruchi Chaudhary, J. Gordon Burleigh, David Fernández-Baca
We present a new method for inferring species trees from multi-copy gene trees. Our method is based on a generalization of the Robinson-Foulds (RF) distance to multi-labeled trees…
Extracting Conflict-free Information from Multi-labeled Trees
Akshay Deepak, David Fernández-Baca, Michelle M. McMahon
A multi-labeled tree, or MUL-tree, is a phylogenetic tree where two or more leaves share a label, e.g., a species name. A MUL-tree can imply multiple conflicting phylogenetic relat…
A Simple Characterization of the Minimal Obstruction Sets for Three-State Perfect Phylogenies
Brad Shutters, David Fernández-Baca
Lam, Gusfield, and Sridhar (2009) showed that a set of three-state characters has a perfect phylogeny if and only if every subset of three characters has a perfect phylogeny. They…
Comparing and Aggregating Partially Resolved Trees
Mukul S. Bansal, Jianrong Dong, David Fernández-Baca
We define, analyze, and give efficient algorithms for two kinds of distance measures for rooted and unrooted phylogenies. For rooted trees, our measures are based on the topologies…