Ancestral Sequence Reconstruction With Maximum Parsimony And Its Accuracy In Mathematical Phylogenetics
DOWNLOAD
Download Ancestral Sequence Reconstruction With Maximum Parsimony And Its Accuracy In Mathematical Phylogenetics PDF/ePub or read online books in Mobi eBooks. Click Download or Read Online button to get Ancestral Sequence Reconstruction With Maximum Parsimony And Its Accuracy In Mathematical Phylogenetics book now. This website allows unlimited access to, at the time of writing, more than 1.5 million titles, including hundreds of thousands of titles in various foreign languages. If the content not found or just blank you must refresh this page
Ancestral Sequence Reconstruction With Maximum Parsimony And Its Accuracy In Mathematical Phylogenetics
DOWNLOAD
Author : Lina Herbst
language : de
Publisher:
Release Date : 2019
Ancestral Sequence Reconstruction With Maximum Parsimony And Its Accuracy In Mathematical Phylogenetics written by Lina Herbst and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019 with categories.
Ancestral Sequence Reconstruction
DOWNLOAD
Author : David A Liberles
language : en
Publisher: OUP Oxford
Release Date : 2007-05-31
Ancestral Sequence Reconstruction written by David A Liberles and has been published by OUP Oxford this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007-05-31 with Science categories.
Ancestral sequence reconstruction is a technique of growing importance in molecular evolutionary biology and comparative genomics. As a powerful tool for testing evolutionary and ecological hypotheses, as well as uncovering the link between sequence and molecular phenotype, there are potential applications in a range of fields. Ancestral Sequence Reconstruction starts with a historical overview of the field, before discussing the potential applications in drug discovery and the pharmaceutical industry. This is followed by a section on computational methodology, which provides a detailed discussion of the available methods for reconstructing ancestral sequences (including their advantages, disadvantages, and potential pitfalls). Purely computational applications of the technique are then covered, including whole proteome reconstruction. Further chapters provide a detailed discussion on taking computationally reconstructed sequences and synthesizing them in the laboratory. The book concludes with a description of the scientific questions where experimental ancestral sequence reconstruction has been utilized to provide insights and inform future research. This research level text provides a first synthesis of the theories, methodologies and applications associated with ancestral sequence recognition, while simultaneously addressing many of the hot topics in the field. It will be of interest and use to both graduate students and researchers in the fields of molecular biology, molecular evolution, and evolutionary bioinformatics.
Mathematics Of Evolution And Phylogeny
DOWNLOAD
Author : Olivier Gascuel
language : en
Publisher: OUP Oxford
Release Date : 2005-02-24
Mathematics Of Evolution And Phylogeny written by Olivier Gascuel and has been published by OUP Oxford this book supported file pdf, txt, epub, kindle and other format this book has been release on 2005-02-24 with Mathematics categories.
This book considers evolution at different scales: sequences, genes, gene families, organelles, genomes and species. The focus is on the mathematical and computational tools and concepts, which form an essential basis of evolutionary studies, indicate their limitations, and give them orientation. Recent years have witnessed rapid progress in the mathematics of evolution and phylogeny, with models and methods becoming more realistic, powerful, and complex. Aimed at graduates and researchers in phylogenetics, mathematicians, computer scientists and biologists, and including chapters by leading scientists: A. Bergeron, D. Bertrand, D. Bryant, R. Desper, O. Elemento, N. El-Mabrouk, N. Galtier, O. Gascuel, M. Hendy, S. Holmes, K. Huber, A. Meade, J. Mixtacki, B. Moret, E. Mossel, V. Moulton, M. Pagel, M.-A. Poursat, D. Sankoff, M. Steel, J. Stoye, J. Tang, L.-S. Wang, T. Warnow, Z. Yang, this book of contributed chapters explains the basis and covers the recent results in this highly topical area.
Bioinformatics And Phylogenetics
DOWNLOAD
Author : Tandy Warnow
language : en
Publisher: Springer
Release Date : 2019-04-08
Bioinformatics And Phylogenetics written by Tandy Warnow and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-04-08 with Computers categories.
This volume presents a compelling collection of state-of-the-art work in algorithmic computational biology, honoring the legacy of Professor Bernard M.E. Moret in this field. Reflecting the wide-ranging influences of Prof. Moret’s research, the coverage encompasses such areas as phylogenetic tree and network estimation, genome rearrangements, cancer phylogeny, species trees, divide-and-conquer strategies, and integer linear programming. Each self-contained chapter provides an introduction to a cutting-edge problem of particular computational and mathematical interest. Topics and features: addresses the challenges in developing accurate and efficient software for the NP-hard maximum likelihood phylogeny estimation problem; describes the inference of species trees, covering strategies to scale phylogeny estimation methods to large datasets, and the construction of taxonomic supertrees; discusses the inference of ultrametric distances from additive distance matrices, and the inference of ancestral genomes under genome rearrangement events; reviews different techniques for inferring evolutionary histories in cancer, from the use of chromosomal rearrangements to tumor phylogenetics approaches; examines problems in phylogenetic networks, including questions relating to discrete mathematics, and issues of statistical estimation; highlights how evolution can provide a framework within which to understand comparative and functional genomics; provides an introduction to Integer Linear Programming and its use in computational biology, including its use for solving the Traveling Salesman Problem. Offering an invaluable source of insights for computer scientists, applied mathematicians, and statisticians, this illuminating volume will also prove useful for graduate courses on computational biology and bioinformatics.
Computational Phylogenetics
DOWNLOAD
Author : Tandy Warnow
language : en
Publisher: Cambridge University Press
Release Date : 2017-11-02
Computational Phylogenetics written by Tandy Warnow and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-11-02 with Computers categories.
This book presents the foundations of phylogeny estimation and technical material enabling researchers to develop improved computational methods.
Inference Of Insertion And Deletion Scenarios For Ancestral Genome Reconstruction And Phylogenetic Analyses
DOWNLOAD
Author : Abdoulaye Diallo
language : en
Publisher:
Release Date : 2009
Inference Of Insertion And Deletion Scenarios For Ancestral Genome Reconstruction And Phylogenetic Analyses written by Abdoulaye Diallo and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009 with categories.
Evaluation Of Phylogeny Reconstruction Algorithms
DOWNLOAD
Author : Dehua Hang
language : en
Publisher:
Release Date : 2005
Evaluation Of Phylogeny Reconstruction Algorithms written by Dehua Hang and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2005 with Branch and bound algorithms categories.
Phylogenetics
DOWNLOAD
Author : Charles Semple
language : en
Publisher: Oxford University Press on Demand
Release Date : 2003
Phylogenetics written by Charles Semple and has been published by Oxford University Press on Demand this book supported file pdf, txt, epub, kindle and other format this book has been release on 2003 with Computers categories.
'Phylogenetics' is the reconstruction and analysis of phylogenetic (evolutionary) trees and networks based on inherited characteristics. It is a flourishing area of intereaction between mathematics, statistics, computer science and biology.The main role of phylogenetic techniques lies in evolutionary biology, where it is used to infer historical relationships between species. However, the methods are also relevant to a diverse range of fields including epidemiology, ecology, medicine, as well as linguistics and cognitive psychologyThis graduate-level book, based on the authors lectures at The University of Canterbury, New Zealand, focuses on the mathematical aspects of phylogenetics. It brings together the central results of the field (providing proofs of the main theorem), outlines their biological significance,and indicateshow algorithms may be derived. The presentation is self-contained and relies on discrete mathematics with some probability theory. A set of exercises and at least one specialist topic ends each chapter.This book is intended for biologists interested in the mathematical theory behind phylogenetic methods, and for mathematicians, statisticians, and computer scientists eager to learn about this emerging area of discrete mathematics.'Phylogenetics' in the 24th volume in the Oxford Lecture Series in Mathematics and its Applications. This series contains short books suitable for graduate students and researchers who want a well-written account of mathematics that is fundamental to current to research. The series emphasises futuredirections of research and focuses on genuine applications of mathematics to finance, engineering and the physical and biological sciences.
Impact Of Molecular Evolutionary Footprints On Phylogenetic Accuracy
DOWNLOAD
Author : Bhakti Dwivedi
language : en
Publisher:
Release Date : 2009
Impact Of Molecular Evolutionary Footprints On Phylogenetic Accuracy written by Bhakti Dwivedi and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009 with Evolution (Biology) categories.
An accurately inferred phylogeny is important to the study of molecular evolution. Factors impacting the accuracy of a phylogenetic tree can be traced to several consecutive steps leading to the inference of the phylogeny. In this simulation-based study our focus is on the impact of the certain evolutionary features of the nucleotide sequences themselves in the alignment rather than any source of error during the process of sequence alignment or due to the choice of the method of phylogenetic inference. Nucleotide sequences can be characterized by summary statistics such as sequence length and base composition. When two or more such sequences need to be compared to each other (as in an alignment prior to phylogenetic analysis) additional evolutionary features come into play, such as the overall rate of nucleotide substitution, the ratio of two specific instantaneous, rates of substitution (rate at which transitions and transversions occur), and the shape parameter, of the gamma distribution (that quantifies the extent of heterogeneity in substitution rate among sites in an alignment). We studied the implications of the following five sequence parameters, individually and in combination: sequence length, substitution rate, nucleotide base composition, the transition-transversion rate ratio and the rate heterogeneity among the sites. It is found that the transition-transversion rate ratio or kappa has a significant impact on phylogenetic accuracy, with a strong positive interaction with accuracy at high substitution rates, contrary to general belief. This work on known expected tree has implications for the researcher in field and would enable them to choose from among the multiple genes typically available today for an accurate phylogenetic inference. DNA sequences diverge from their ancestral sequences by means of evolutionary events (other than mentioned above) such as deletion (deletion of one more nucleotide from a sequence) or insertion (insertion of one more nucleotide to a sequence) events, commonly referreed to as gaps in a sequence alignment. We have also investigated the relationship between the number of gaps and phylogenetic accuracy, when the gaps are introduced in an alignment to reflect indel (insertion/deletion) events during the evolution of DNA sequences. DNA sequence alignments were generated using computer simulation, while varying several sequence parameters and introducing both substitution and insertion/deletion events, along a 16-taxon model tree, and systematically varying the expected proportion of gapped sites. The resulting alignments were subjected to commonly used gap treatment methods and methods of phylogenetic inference. The results showed that in general, there is a strong almost deterministic relationship between the amount of gap in the data and the level of phylogenetic accuracy, when the amount of gap was high. Our results also suggest that, as long as the gaps in the alignment are a consequence of indel events in the evolutionary history of the sequences, the accuracy of phylogenetic analysis is likely to improve if alignment gaps are categorized as arising from insertion events or deletion events and then treated separately in the analysis and if the phylogenetic signal provided by indels is harnessed, for example, by treating the gaps as binary characters in Bayesian or Maximum Parsimony analyses, or in an integrated manner along with substitution events.
Parsimony Phylogeny And Genomics
DOWNLOAD
Author : Victor A. Albert
language : en
Publisher: OUP Oxford
Release Date : 2005-03-24
Parsimony Phylogeny And Genomics written by Victor A. Albert and has been published by OUP Oxford this book supported file pdf, txt, epub, kindle and other format this book has been release on 2005-03-24 with Science categories.
Parsimony analysis (cladistics) has long been one of the most widely used methods of phylogenetic inference in the fields of systematic and evolutionary biology. Moreover it has mathematical attributes that lend itself for use with complex, genomic-scale data sets. This book demonstrates the potential that this powerful hierarchical data summarization method also has for both structural and functional comparative genomic research.
