34 Result(s)
within
Chapter
David Fernández-Baca
-
Chapter and Conference Paper
Testing the Agreement of Trees with Internal Labels
The input to the agreement problem is a collection \(\mathcal {P}= \{\mathcal {T}_1, \mathcal {T}_2, \dots , \mathcal {T}_k\}\) of phylogenetic trees, called input trees, over partially overlap** sets of taxa...
-
Chapter and Conference Paper
Checking Phylogenetic Decisiveness in Theory and in Practice
Suppose we have a set X consisting of n taxa and we are given information from k loci from which to construct a phylogeny for X. Each locus offers information for only a fraction of the taxa. The question is whet...
-
Chapter and Conference Paper
Fast Compatibility Testing for Phylogenies with Nested Taxa
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 labeled Rodentia, which itself could n...
-
Chapter and Conference Paper
Constructing and Employing Tree Alignment Graphs for Phylogenetic Synthesis
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 account for nested taxonomic re...
-
Chapter and Conference Paper
Characterizing Compatibility and Agreement of Unrooted Trees via Cuts in Graphs
Deciding whether there is a single tree —a supertree— that summarizes the evolutionary information in a collection of unrooted trees is a fundamental problem in phylogenetics. We consider two versions of this ...
-
Chapter and Conference Paper
Improved Lower Bounds on the Compatibility of Quartets, Triplets, and Multi-state Characters
We study a long standing conjecture on the necessary and sufficient conditions for the compatibility of multi-state characters: There exists a function f(r) such that, for any set C of r-state characters, C is co...
-
Chapter and Conference Paper
Fixed-Parameter Algorithms for Finding Agreement Supertrees
We study the agreement supertree approach for combining rooted phylogenetic trees when the input trees do not fully agree on the relative positions of the taxa. Two approaches to dealing with such conflicting ...
-
Chapter and Conference Paper
Identifying Rogue Taxa through Reduced Consensus: NP-Hardness and Exact Algorithms
A rogue taxon in a collection of phylogenetic trees is one whose position varies drastically from tree to tree. The presence of such taxa can greatly reduce the resolution of the consensus tree (e.g., the majo...
-
Chapter and Conference Paper
Extracting Conflict-Free Information from Multi-labeled Trees
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 relationships for the same set of ...
-
Chapter and Conference Paper
Fast Local Search for Unrooted Robinson-Foulds Supertrees
A Robinson-Foulds (RF) supertree for a collection of input trees is a comprehensive species phylogeny that is at minimum total RF distance to the input trees. Thus, an RF supertree is consistent with the maxim...
-
Chapter and Conference Paper
Constructing Large Conservative Supertrees
Generalizations of the strict and loose consensus methods to the supertree setting, recently introduced by McMorris and Wilkinson, are studied. The supertrees these methods produce are conservative in the sens...
-
Chapter and Conference Paper
Constructing Majority-Rule Supertrees
Supertree methods combine the phylogenetic information from multiple partially-overlap** trees into a larger phylogenetic tree called a supertree. Several supertree construction methods have been proposed to...
-
Chapter and Conference Paper
Generalized Binary Tanglegrams: Algorithms and Applications
Several applications require the joint display of two phylogenetic trees whose leaves are matched by inter-tree edges. This issue arises, for example, when comparing gene trees and species trees or when studyi...
-
Chapter and Conference Paper
Comparing and Aggregating Partially Resolved Trees
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 the input trees induce on tripl...
-
Chapter and Conference Paper
Parametric Analysis for Ungapped Markov Models of Evolution
We present efficient sensitivity-analysis algorithms for two problems involving Markov models of sequence evolution: ancestral reconstruction in evolutionary trees and local ungapped alignment under log-odds s...
-
Chapter
MRF Supertrees
We survey and present new results and techniques for the supertree method matrix representation using flip** (MRF). The method resolves inconsistencies among the input trees by working with the matrix represent...
-
Chapter and Conference Paper
Supertrees by Flip**
The input to a supertree problem is a collection of phyloge-netic trees that intersect pairwise in their leaf sets; the goal is to construct a single tree that retains as much as possible of the information in...
-
Chapter and Conference Paper
Inverse Parametric Sequence Alignment
We consider the inverse parametric sequence alignment problem, where a sequence alignment is given and the task is to determine parameter values such that the given alignment is optimal at that parameter setti...
-
Chapter
The Perfect Phylogeny Problem
A phylogeny is a tree representation of the evolutionary history of a set of taxa (organisms, biological sequences, populations, or languages). Thus, phylogeny construction is among the basic computational proble...
-
Chapter and Conference Paper
Multi-parameter Minimum Spanning Trees
A framework for solving certain multidimensional parametric search problems in randomized linear time is presented, along with its application to optimization on matroids, including parametric minimum spanning...
