Phylogenetic Supertrees PDF Download
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Author | : O. R. P. Bininda-Emonds |
Publisher | : Springer Science & Business Media |
Total Pages | : 568 |
Release | : 2004-08-25 |
Genre | : Computers |
ISBN | : 9781402023293 |
Download Phylogenetic Supertrees Book in PDF, ePub and Kindle
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 | : Olaf R.P. Bininda-Emonds |
Publisher | : Springer Science & Business Media |
Total Pages | : 547 |
Release | : 2004-05-31 |
Genre | : Science |
ISBN | : 1402023308 |
Download Phylogenetic Supertrees Book in PDF, ePub and Kindle
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 | : Markus Fleischauer |
Publisher | : |
Total Pages | : 0 |
Release | : 2018 |
Genre | : |
ISBN | : |
Download Fast and Accurate Supertrees Book in PDF, ePub and Kindle
Phylogenetics is the study of evolutionary relationships between biological entities; phylogenetic trees (phylogenies) are a visualization of these evolutionary relationships. Accurate approaches to reconstruct hylogenies from sequence data usually result in NPhard optimization problems, hence local search heuristics have to be applied in practice. These methods are highly accurate and fast enough as long as the input data is not too large. Divide-and-conquer techniques are a promising approach to boost scalability and accuracy of those local search heuristics on very large datasets. A divide-and-conquer method breaks down a large phylogenetic problem into smaller sub-problems that are computationally easier to solve. The sub-problems (overlapping trees) are then combined using a supertree method. Supertree methods merge a set of overlapping phylogenetic trees into a supertree containing all taxa of the input trees. The challenge in supertree reconstruction is the way of dealing with conflicting information in the input trees. Many different algorithms for different objective functions have been suggested to resolve these conflicts. In particular, there are methods that encode the source trees in a matrix and the supertree is constructed applying a local search heuristic to optimize the respective objective function. The most widely used supertree methods use such local search heuristics. However, to really improve the scalability of accurate tree reconstruction by divide-and-conquer approaches, accurate polynomial time methods are needed for the supertree reconstruction step. In this work, we present approaches for accurate polynomial time supertree reconstruction in particular Bad Clade Deletion (BCD), a novel heuristic supertree algorithm with polynomial running time. BCD uses minimum cuts to greedily delete a locally minimal number of columns from a matrix representation to make it compatible. Different from local search heuristics, it guarantees to return the directed perfect phylogeny for the input matrix, corresponding to the parent tree of the input trees if one exists. BCD can take support values of the source trees into account without an increase in complexity. We show how reliable clades can be used to restrict the search space for BCD and how those clades can be collected from the input data using the Greedy Strict Consensus Merger. Finally, we introduce a beam search extension for the BCD algorithm that keeps alive a constant number of partial solutions in each top-down iteration phase. The guaranteed worst-case running time of BCD with beam search extension is still polynomial. We present an exact and a randomized subroutine to generate suboptimal partial solutions. In our thorough evaluation on several simulated and biological datasets against a representative set of supertree methods we found that BCD is more accurate than the most accurate supertree methods when using support values and search space restriction on simulated data. Simultaneously BCD is faster than any other evaluated method. The beam search approach improved the accuracy of BCD on all evaluated datasets at the cost of speed. We found that BCD supertrees can boost maximum likelihood tree reconstruction when used as starting tree. Further, BCD could handle large scale datasets where local search heuristics did not converge in reasonable time. Due to its combination of speed, accuracy, and the ability to reconstruct the parent tree if one exists, BCD is a promising approach to enable outstanding scalability of divide-and-conquer approaches.
Author | : Helen Marie Shearman |
Publisher | : |
Total Pages | : 220 |
Release | : 2013 |
Genre | : Biodiversity |
ISBN | : |
Download Novel Phylogenetic Methods Book in PDF, ePub and Kindle
Author | : |
Publisher | : |
Total Pages | : 404 |
Release | : 2007 |
Genre | : Animals |
ISBN | : |
Download Zoological Studies Book in PDF, ePub and Kindle
Author | : Jianrong Dong |
Publisher | : |
Total Pages | : 128 |
Release | : 2012 |
Genre | : |
ISBN | : |
Download Constructing Liberal and Conservative Supertrees and Exact Solutions for Reduced Consensus Problems Book in PDF, ePub and Kindle
Author | : Tandy Warnow |
Publisher | : Springer |
Total Pages | : 410 |
Release | : 2019-04-08 |
Genre | : Computers |
ISBN | : 3030108376 |
Download Bioinformatics and Phylogenetics Book in PDF, ePub and Kindle
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.
Author | : |
Publisher | : |
Total Pages | : 542 |
Release | : 2008 |
Genre | : Biology |
ISBN | : |
Download Proceedings Book in PDF, ePub and Kindle
Author | : Michelle Dawn Swenson |
Publisher | : |
Total Pages | : 260 |
Release | : 2009 |
Genre | : |
ISBN | : |
Download Phylogenetic Supertree Methods Book in PDF, ePub and Kindle
The central task in phylogenetics is to infer the evolutionary relationships among a given set of species. These relationships are usually represented by a phylogenetic tree with the species of interest at the leaves and where the internal vertices of the tree represent ancestral species. The amount of available molecular data is increasing exponentially and, given the continual advances in sequencing techniques and throughput, this explosive growth will likely continue. These vast amounts of available data mean that biologists are able to assemble large multi-gene datasets for use in phylogenetic analyses, which presents distinct computational challenges. Supertree methods comprise one approach to reconstructing large phylogenies, given estimated trees for overlapping subsets of the entire set of taxa. These source trees are combined into a single supertree on the full set of taxa using various algorithmic techniques. When the data allow, the competing approach is a combined analysis (also known as a "super-matrix" or "total evidence" approach), whereby the different sequence data matrices for each of the different subsets of taxa are put into a single super-matrix, and a tree is estimated on that super-matrix. In this dissertation, I present simulation software I designed to allow users to compare the relative performance of different supertree methods, as well as that of combined analysis, on more realistic data and on a larger scale than has been used up to this point. I present an extensive simulation study that uses this software to compare the performance of supertree methods and combined analysis, and that demonstrates a need for more topologically accurate supertree methods. I also introduce a new supertree method that I have developed that outperforms the most commonly used, and what until now has arguably been the most accurate, supertree method.
Author | : |
Publisher | : |
Total Pages | : 260 |
Release | : 2008 |
Genre | : Historical geology |
ISBN | : |
Download Zitteliana Book in PDF, ePub and Kindle