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BIOINFORMATICS
2002
100views more  BIOINFORMATICS 2002»
11 years 1 months ago
Optimal algorithms for local vertex quartet cleaning
Reconstructing evolutionary trees is an important problem in biology. A response to the computational intractability of most of the traditional criteria for inferring evolutionary...
Gianluca Della Vedova, Todd Wareham
BMCBI
2008
139views more  BMCBI 2008»
11 years 1 months ago
A topological transformation in evolutionary tree search methods based on maximum likelihood combining p-ECR and neighbor joinin
Background: Inference of evolutionary trees using the maximum likelihood principle is NP-hard. Therefore, all practical methods rely on heuristics. The topological transformations...
Maozu Guo, Jian-Fu Li, Yang Liu
METMBS
2004
140views Mathematics» more  METMBS 2004»
11 years 2 months ago
New Techniques for Generation and Analysis of Evolutionary Trees
We introduce new distance measures for the construction and analysis of phylogenies, focusing on thioredoxin-fold proteins. Our distance measures for tree construction are based o...
Chang Wang, Stephen D. Scott, Qingping Tao, Dmitri...
NIPS
2008
11 years 2 months ago
Efficient Inference in Phylogenetic InDel Trees
Accurate and efficient inference in evolutionary trees is a central problem in computational biology. While classical treatments have made unrealistic site independence assumption...
Alexandre Bouchard-Côté, Michael I. J...
STOC
1996
ACM
92views Algorithms» more  STOC 1996»
11 years 5 months ago
Constructing Evolutionary Trees in the Presence of Polymorphic Characters
Abstract. Most phylogenetics literature and construction methods based upon characters presume monomorphism (one state per character per species), yet polymorphism (multiple states...
Maria Luisa Bonet, Cynthia A. Phillips, Tandy Warn...
ISAAC
2001
Springer
125views Algorithms» more  ISAAC 2001»
11 years 5 months ago
Computing the Quartet Distance between Evolutionary Trees in Time O(n log2 n)
Evolutionary trees describing the relationship for a set of species are central in evolutionary biology, and quantifying diļ¬€erences between evolutionary trees is an important tas...
Gerth Stølting Brodal, Rolf Fagerberg, Chri...
BIBM
2008
IEEE
134views Bioinformatics» more  BIBM 2008»
11 years 7 months ago
New Approaches to Compare Phylogenetic Search Heuristics
We present new and novel insights into the behavior of two maximum parsimony heuristics for building evolutionary trees of different sizes. First, our results show that the heuris...
Seung-Jin Sul, Suzanne Matthews, Tiffani L. Willia...
BICOB
2009
Springer
11 years 8 months ago
A Fitness Distance Correlation Measure for Evolutionary Trees
Phylogenetics is concerned with inferring the genealogical relationships between a group of organisms (or taxa), and this relationship is usually expressed as an evolutionary tree....
Hyun Jung Park, Tiffani L. Williams
LATA
2009
Springer
11 years 8 months ago
From Gene Trees to Species Trees through a Supertree Approach
Abstract. Gene trees are leaf-labeled trees inferred from molecular sequences. Due to duplication events arising in genome evolution, gene trees usually have multiple copies of som...
Celine Scornavacca, Vincent Berry, Vincent Ranwez
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