Short Quartet Puzzling: A New Quartet-Based Phylogeny Reconstruction Algorithm
نویسندگان
چکیده
منابع مشابه
Short Quartet Puzzling: A New Quartet-Based Phylogeny Reconstruction Algorithm
Quartet-based phylogeny reconstruction methods, such as Quartet Puzzling, were introduced in the hope that they might be competitive with maximum likelihood methods, without being as computationally intensive. However, despite the numerous quartet-based methods that have been developed, their performance in simulation has been disappointing. In particular, Ranwez and Gascuel, the developers of ...
متن کاملOn a New Quartet-Based Phylogeny Reconstruction Algorithm
Recently we developed a new quartet-based algorithm for phylogenetic analysis [22]. This algorithm constructs a limited number of trees for a given set of DNA or protein sequences and the initial experimental results show that the probability for the correct tree to be included in this small set of trees is very high. In this paper we further extend the idea. We first discuss a revision to the ...
متن کاملQuartet-Based Phylogeny Reconstruction from Gene Orders
Phylogenetic reconstruction from gene-rearrangement data is attracting increasing attention from biologists and computer scientists. Methods used in reconstruction include distance-based methods, parsimony methods using sequence encodings, and direct optimization. The latter, pioneered by Sankoff and extended by us with the software suite GRAPPA, is the most accurate approach; however, its exha...
متن کاملQuartet Puzzling: A Quartet Maximum-Likelihood Method for Reconstructing Tree Topologies
A versatile method, quartet puzzling, is introduced to reconstruct the topology (branching pattern) of a phylogenetic tree based on DNA or amino acid sequence data. This method applies maximum-likelihood tree reconstruction to all possible quartets that can be formed from n sequences. The quartet trees serve as starting points to reconstruct a set of optimal n-taxon trees. The majority rule con...
متن کاملQuartet methods for phylogeny reconstruction from gene orders
Phylogenetic reconstruction from gene-rearrangement data has attracted increasing attention from biologists and computer scientists. Methods used in reconstruction include distance-based methods, parsimony methods using sequence-based encodings, and direct optimization. The latter, pioneered by Sankoff and extended by us with the software suite GRAPPA, is the most accurate approach; however, it...
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ژورنال
عنوان ژورنال: Journal of Computational Biology
سال: 2008
ISSN: 1066-5277,1557-8666
DOI: 10.1089/cmb.2007.0103