Algorithms for Quartet Based Phylogeny Reconstruction PDF Download
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Author: Gang Wu
Publisher:
ISBN:
Category : Computer algorithms
Languages : en
Pages : 79
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Author: Gang Wu
Publisher:
ISBN:
Category : Computer algorithms
Languages : en
Pages : 79
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Author: Jakub Truszkowski
Publisher:
ISBN:
Category :
Languages : en
Pages : 135
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Book Description
One of the most fundamental computational problems in biology is that of inferring evolutionary histories of groups of species from sequence data. Such evolutionary histories, known as phylogenies are usually represented as binary trees where leaves represent extant species, whereas internal nodes represent their shared ancestors. As the amount of sequence data available to biologists increases, very fast phylogenetic reconstruction algorithms are becoming necessary. Currently, large sequence alignments can contain up to hundreds of thousands of sequences, making traditional methods, such as Neighbor Joining, computationally prohibitive. To address this problem, we have developed three novel fast phylogenetic algorithms. The first algorithm, QTree, is a quartet-based heuristic that runs in O(n log n) time. It is based on a theoretical algorithm that reconstructs the correct tree, with high probability, assuming every quartet is inferred correctly with constant probability. The core of our algorithm is a balanced search tree structure that enables us to locate an edge in the tree in O(log n) time. Our algorithm is several times faster than all the current methods, while its accuracy approaches that of Neighbour Joining. The second algorithm, LSHTree, is the first sub-quadratic time algorithm with theoretical performance guarantees under a Markov model of sequence evolution. Our new algorithm runs in O(n^{1+[gamma](g)} log^2 n) time, where [gamma] is an increasing function of an upper bound on the mutation rate along any branch in the phylogeny, and [gamma](g)
Author: Vincent Moulton
Publisher: Springer Science & Business Media
ISBN: 3642152937
Category : Computers
Languages : en
Pages : 385
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Book Description
This book constitutes the refereed proceedings of the 10th International Workshop on Algorithms in Bioinformatics, WABI 2010, held in Liverpool, UK, in September 2010. The 30 revised full papers presented were carefully reviewed and selected from 83 submissions. The papers are organized in topical sections on biomolecular structure: RNA, protein and molecular comparison; comparative genomics; haplotype and genotype analysis; high-throughput data analysis: next generation sequencing and flow cytometry; networks; phylogenetics; and sequences, strings and motifs.
Author: Thomas Dencker
Publisher:
ISBN:
Category : Phylogeny
Languages : en
Pages :
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Author: Teresa M. Przytycka
Publisher: Springer
ISBN: 3642230385
Category : Computers
Languages : en
Pages : 388
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Book Description
This book constitutes the refereed proceedings of the 11th International Workshop on Algorithms in Bioinformatics, WABI 2011, held in Saarbrücken, Germany, in September 2011. The 30 papers presented were carefully reviewed and selected from 77 submissions. They cover aspects of algorithms in bioinformatics, computational biology and systems biology.
Author: Lei Xin
Publisher:
ISBN:
Category :
Languages : en
Pages : 250
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Author: Olaf R.P. Bininda-Emonds
Publisher: Springer Science & Business Media
ISBN: 1402023308
Category : Science
Languages : en
Pages : 547
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Book Description
This is the first book on "phylogenetic supertrees", a recent, but controversial development for inferring evolutionary trees. Rather than analyze the combined primary character data directly, supertree construction proceeds by combining the tree topologies derived from those data. This difference in strategy has allowed for the exciting possibility of larger, more complete phylogenies than are otherwise currently possible, with the potential to revolutionize evolutionarily-based research. This book provides a comprehensive look at supertrees, ranging from the methods used to build supertrees to the significance of supertrees to bioinformatic and biological research. Reviews of many the major supertree methods are provided and four new techniques, including a Bayesian implementation of supertrees, are described for the first time. The far-reaching impact of supertrees on biological research is highlighted both in general terms and through specific examples from diverse clades such as flowering plants, even-toed ungulates, and primates. The book also critically examines the many outstanding challenges and problem areas for this relatively new field, showing the way for supertree construction in the age of genomics. Interdisciplinary contributions from the majority of the leading authorities on supertree construction in all areas of the bioinformatic community (biology, computer sciences, and mathematics) will ensure that this book is a valuable reference with wide appeal to anyone interested in phylogenetic inference.
Author: Haoyong Zhang
Publisher:
ISBN:
Category :
Languages : en
Pages : 150
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Author: David Sankoff
Publisher: World Scientific
ISBN: 1860947832
Category : Science
Languages : en
Pages : 391
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Book Description
High-throughput sequencing and functional genomics technologies have given us the human genome sequence as well as those of other experimentally, medically, and agriculturally important species, and have enabled large-scale genotyping and gene expression profiling of human populations. Databases containing large numbers of sequences, polymorphisms, structures, and gene expression profiles of normal and diseased tissues are being rapidly generated for human and model organisms. Bioinformatics is thus rapidly growing in importance in the annotation of genomic sequences; the understanding of the interplay among and between genes and proteins; the analysis of genetic variability of species; the identification of pharmacological targets; and the inference of evolutionary origins, mechanisms, and relationships. This proceedings volume contains an up-to-date exchange of knowledge, ideas, and solutions to conceptual and practical issues of bioinformatics by researchers, professionals, and industrial practitioners at the 5th Asia-Pacific Bioinformatics Conference held in Hong Kong in January 2007.
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Author: Bourque, Guillaume
Publisher: Ann Arbor, Mich. : University Microfilms International
ISBN:
Category :
Languages : en
Pages : 190
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