12 Result(s)
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Article
David Fernández-Baca
English
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Article
Open AccessTesting the agreement of trees with internal labels
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...
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Open AccessAn efficient algorithm for testing the compatibility of phylogenies with nested taxa
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 ...
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Editorial
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Open AccessEnumerating all maximal frequent subtrees in collections of phylogenetic trees
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...
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Open AccessCharacterizing 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 ...
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Open AccessInferring species trees from incongruent multi-copy gene trees using the Robinson-Foulds distance
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...
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Open AccessExtracting 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 ...
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Open AccessIncompatible quartets, triplets, and 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...
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Open AccessiGTP: A software package for large-scale gene tree parsimony analysis
The ever-increasing wealth of genomic sequence information provides an unprecedented opportunity for large-scale phylogenetic analysis. However, species phylogeny inference is obfuscated by incongruence among ...
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Open AccessRobinson-Foulds Supertrees
Supertree methods synthesize collections of small phylogenetic trees with incomplete taxon overlap into comprehensive trees, or supertrees, that include all taxa found in the input trees. Supertree methods bas...
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Open AccessConstructing 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...
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Open AccessPhyloFinder: An intelligent search engine for phylogenetic tree databases
Bioinformatic tools are needed to store and access the rapidly growing phylogenetic data. These tools should enable users to identify existing phylogenetic trees containing a specified taxon or set of taxa and...
