LATIN 2012: Theoretical Informatics
10th Latin American Symposium, Arequipa, Peru, April 16-20, 2012. Proceedings
Article
A semi-labeled tree is a tree where all leaves as well as, possibly, some internal nodes are labeled with taxa. Semi-labeled trees encompass ordinary phylogenetic trees and taxonomies. Suppose we are given a c...
Chapter and Conference Paper
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
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...
Article
We present a new graph-based approach to the following basic problem in phylogenetic tree construction. Let $$\mathcal {P}= \{T_1, \ld...
Article
Semi-labeled trees generalize ordinary phylogenetic trees, allowing internal nodes to be labeled by higher-order taxa. Taxonomies are examples of semi-labeled trees. Suppose we are given collection ...
Chapter and Conference Paper
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
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...
Article
The problem of mining collections of trees to identify common patterns, called frequent subtrees (FSTs), arises often when trying to interpret the results of phylogenetic analysis. FST mining generalizes the w...
Article
Article
A common problem in phylogenetic analysis is to identify frequent patterns in a collection of phylogenetic trees. The goal is, roughly, to find a subset of the species (taxa) on which all or some significant s...
Article
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 ...
Article
Constructing species trees from multi-copy gene trees remains a challenging problem in phylogenetics. One difficulty is that the underlying genes can be incongruent due to evolutionary processes such as gene d...
Article
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 ...
Article
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
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 ...
Book and Conference Proceedings
10th Latin American Symposium, Arequipa, Peru, April 16-20, 2012. Proceedings
Chapter and Conference Paper
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
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
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
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 ...