Alignment-free Phylogeny Reconstruction Based On Quartet Trees PDF Download
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Author: Thomas Dencker
Publisher:
ISBN:
Category : Phylogeny
Languages : en
Pages :
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Author: Thomas Dencker
Publisher:
ISBN:
Category : Phylogeny
Languages : en
Pages :
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Author: Kevin Jensen Liu
Publisher:
ISBN:
Category :
Languages : en
Pages : 458
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Phylogenetics is the study of evolutionary relationships. Phylogenetic trees and alignments play important roles in a wide range of biological research, including reconstruction of the Tree of Life - the evolutionary history of all organisms on Earth - and the development of vaccines and antibiotics. Today's phylogenetic studies seek to reconstruct trees and alignments on a greater number and variety of organisms than ever before, primarily due to exponential growth in affordable sequencing and computing power. The importance of phylogenetic trees and alignments motivates the need for methods to reconstruct them accurately and efficiently on large-scale datasets. Traditionally, phylogenetic studies proceed in two phases: first, an alignment is produced from biomolecular sequences with differing lengths, and, second, a tree is produced using the alignment. My dissertation presents the first empirical performance study of leading two-phase methods on datasets with up to hundreds of thousands of sequences. Relatively accurate alignments and trees were obtained using methods with high computational requirements on datasets with a few hundred sequences, but as datasets grew past 1000 sequences and up to tens of thousands of sequences, the set of methods capable of analyzing a dataset diminished and only the methods with the lowest computational requirements and lowest accuracy remained. Alternatively, methods have been developed to simultaneously estimate phylogenetic alignments and trees. Methods optimizing the treelength optimization problem - the most widely-used approach for simultaneous estimation - have not been shown to return more accurate trees and alignments than two-phase approaches. I demonstrate that treelength optimization under a particular class of optimization criteria represents a promising means for inferring accurate trees and alignments. The other methods for simultaneous estimation are not known to support analyses of datasets with a few hundred sequences due to their high computational requirements. The main contribution of my dissertation is SATe, the first fast and accurate method for simultaneous estimation of alignments and trees on datasets with up to several thousand nucleotide sequences. SATe improves upon the alignment and topological accuracy of all existing methods, especially on the most difficult-to-align datasets, while retaining reasonable computational requirements.
Author: Barry G. Hall
Publisher: Sinauer Associates, Incorporated
ISBN:
Category : Science
Languages : en
Pages : 258
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Barry G. Hall helps beginners get started in creating phylogenetic trees from protein or nucleic acid sequence data.
Author: Nakhleh, Luay
Publisher:
ISBN:
Category : Language Arts & Disciplines
Languages : en
Pages : 17
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Researchers interested in the history of the Indo-European family of languages have used a variety of methods to estimate the phylogeny of the family, and have obtained widely differing results. In this paper we explore the reconstructions of the Indo-European phylogeny obtained by using the major phylogeny estimation procedures on an existing database of 336 characters (including lexical, phonological, and morphological characters) for 24 Indo-European languages. Our study finds that the different methods agree in part, but that there are also several striking differences. We discuss the reasons for these differences, and make proposals with respect to phylogenetic reconstruction in historical linguistics.
Author: Gang Wu
Publisher:
ISBN:
Category : Computer algorithms
Languages : en
Pages : 79
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Author: Robert W. Scotland
Publisher: Clarendon Press
ISBN:
Category : Science
Languages : en
Pages : 384
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Phylogenetic reconstruction--the method by which biologists examine the relationship between living and extinct organisms in an effort to identify evolutionary pathways--has seen radical changes in the last ten years. But as rapid advances in mathematical, molecular, developmental, and cladistic techniques have greatly improved reconstruction efforts, they have also sparked controversy, especially with regard to the assumptions and data underlying the cladistic method. This book brings together contributions from a wide range of practitioners in order to find common ground. By examining numerous models from a variety of fields, the book serves as a guide to the latest methods of classification and phylogeny reconstruction and provides insights into the relative merits that each approach has to offer. In particular, developmental studies emerge as a significant factor in cladogram construction. Splendidly written and wide-ranging in scope, Models in Phylogeny Reconstruction will be welcomed by students and researchers in systematic and evolutionary biology.
Author: Paul H. Harvey
Publisher: Oxford University Press, USA
ISBN:
Category : Science
Languages : en
Pages : 376
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Book Description
Recent advances in molecular genetics make the sequencing of genes a straightforward exercise. Comparisons of sequenced genes from different individuals of a species, or from different species, allow the construction of family trees or evolutionary trees which reveal genetic relationships.This volume shows for the first time how those trees, or phylogenies, can be used to answer questions about population dynamics, epidemiology, development, biodiversity, conservation, and the evolution of genetic systems. The techniques for deciding what these new trees can tell us come together ina unified framework so that a common set of methods can be applied, whatever area of biology interests the researcher.
Author: Marc Sabaté Vidales
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Els arbres filogenètics ajuden a modelitzar l'evolució de les espècies. En aquests arbres, les fulles representen les espècies actuals, l'arrel representa l'ancestre comú a totes aquestes espècies i cada branca un procés d'especiació. Per a poder inferir les relacions filogenètiques d'un conjunt d'espècies actuals, podem aspirar a conèixer el genoma d'aquestes espècies, tot i que no disposem d'informació del genoma dels ancestres d'aquestes espècies. Existeix un bon nombre de mètodes de reconstrucció filogenètica. En aquest treball, hem implementat i hem analitzat els resultats de 12 mètodes de reconstrucció per quartets. En aquests mètodes, donat un conjunt d'espècies actuals, s'infereixen les relacions filogenètiqes entre tots els subconjunts de 4 espècies dins del conjunt original, i a continuació es combina tota aquesta informació per a construir l'arbre filogenètic resultant. . Tècniques algebraiques desenvolupades recentment permeten usar el rang de certes matrius per a reconstruir l'arbre filogenètic d'un conjunt d'espècies. En aquest projecte s'usaran aquestes tècniques dins de mètodes de reconstrucció filogenètica basats en quartets. S'implementaran diferents mètodes de quartets i es faran tests per avaluar l'eficàcia dels mètodes.
![Algorithms for Phylogenetic Tree Reconstruction Based on Genome Rearrangements [microform] PDF](https://books.google.com/books/content/images/frontcover/iRkXNAEACAAJ?fife=w80-h100)
Author: Bourque, Guillaume
Publisher: Ann Arbor, Mich. : University Microfilms International
ISBN:
Category :
Languages : en
Pages : 190
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Author: Ryan M. Potter
Publisher:
ISBN:
Category : Phylogeny
Languages : en
Pages : 56
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