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Article
Open AccessInferring phylogenies with incomplete data sets: a 5-gene, 567-taxon analysis of angiosperms
Phylogenetic analyses of angiosperm relationships have used only a small percentage of available sequence data, but phylogenetic data matrices often can be augmented with existing data, especially if one allow...
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Article
Open AccessTriplet supertree heuristics for the tree of life
There is much interest in develo** fast and accurate supertree methods to infer the tree of life. Supertree methods combine smaller input trees with overlap** sets of taxa to make a comprehensive phylogene...
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Article
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...
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Chapter and Conference Paper
Locating Multiple Gene Duplications through Reconciled Trees
We introduce the first exact and efficient algorithm for Guigó et al.’s problem that given a collection of rooted, binary gene trees and a rooted, binary species tree, determines a minimum number of locations ...
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Chapter and Conference Paper
Heuristics for the Gene-Duplication Problem: A Θ(n) Speed-Up for the Local Search
The gene-duplication problem is to infer a species supertree from a collection of gene trees that are confounded by complex histories of gene duplications. This problem is NP-hard and thus requires efficient a...
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Chapter
Quartet Supertrees
We introduce two supertree methods that produce unrooted supertrees from unrooted input trees. The methods assemble supertrees from a weighted quartet (four-taxon) tree representation of the input trees. The f...
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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...
