Problems Of Phylogenetic Reconstruction
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Problems Of Phylogenetic Reconstruction
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Author : Systematics Association
language : en
Publisher: Academic Press
Release Date : 1982
Problems Of Phylogenetic Reconstruction written by Systematics Association and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 1982 with Science categories.
Problems Of Phylogenetic Reconstruction
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Author : K. A. Joysey
language : en
Publisher:
Release Date : 1982
Problems Of Phylogenetic Reconstruction written by K. A. Joysey and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 1982 with categories.
Problems Of Phylogeny Reconstruction From Morphological Data
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Author : Susan Fay Lipson
language : en
Publisher:
Release Date : 1985
Problems Of Phylogeny Reconstruction From Morphological Data written by Susan Fay Lipson and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 1985 with Phylogeny categories.
Methods Of Phylogenetic Reconstruction
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Author : Colin Patterson
language : en
Publisher:
Release Date : 1982
Methods Of Phylogenetic Reconstruction written by Colin Patterson and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 1982 with categories.
Models In Phylogeny Reconstruction
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Author : Robert W. Scotland
language : en
Publisher: Clarendon Press
Release Date : 1994
Models In Phylogeny Reconstruction written by Robert W. Scotland and has been published by Clarendon Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 1994 with Science categories.
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.
Computational Issues In Phylogenetic Reconstruction
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Author : Sagi Snir
language : en
Publisher:
Release Date : 2004
Computational Issues In Phylogenetic Reconstruction written by Sagi Snir and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2004 with categories.
Reconstructing The Tree Of Life
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Author : Trevor R. Hodkinson
language : en
Publisher: CRC Press
Release Date : 2006-12-26
Reconstructing The Tree Of Life written by Trevor R. Hodkinson and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2006-12-26 with Mathematics categories.
To document the world's diversity of species and reconstruct the tree of life we need to undertake some simple but mountainous tasks. Most importantly, we need to tackle species rich groups. We need to collect, name, and classify them, and then position them on the tree of life. We need to do this systematically across all groups of organisms and b
Problems Of Phylogenetic Reconstruction
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Author : Systematics Association
language : en
Publisher: Academic Press
Release Date : 1982
Problems Of Phylogenetic Reconstruction written by Systematics Association and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 1982 with Science categories.
Gene Order Rearrangement Methods For The Reconstruction Of Phylogeny
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Author :
language : de
Publisher:
Release Date : 2006
Gene Order Rearrangement Methods For The Reconstruction Of Phylogeny written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2006 with categories.
The study of phylogeny, i.e. the evolutionary history of species, is a central problem in biology and a key for understanding characteristics of contemporary species. Many problems in this area can be formulated as combinatorial optimisation problems which makes it particularly interesting for computer scientists. The reconstruction of the phylogeny of species can be based on various kinds of data, e.g. morphological properties or characteristics of the genetic information of the species. Maximum parsimony is a popular and widely used method for phylogenetic reconstruction aiming for an explanation of the observed data requiring the least evolutionary changes. A certain property of the genetic information gained much interest for the reconstruction of phylogeny in recent time: the organisation of the genomes of species, i.e. the arrangement of the genes on the chromosomes. But the idea to reconstruct phylogenetic information from gene arrangements has a long history. In Dobzhansky and Sturtevant (1938) it was already pointed out that "a comparison of the different gene arrangements in the same chromosome may, in certain cases, throw light on the historical relationships of these structures, and consequently on the history of the species as a whole". This kind of data is promising for the study of deep evolutionary relationships because gene arrangements are believed to evolve slowly (Rokas and Holland, 2000). This seems to be the case especially for mitochondrial genomes which are available for a wide range of species (Boore, 1999). The development of methods for the reconstruction of phylogeny from gene arrangement data has made considerable progress during the last years. Prominent examples are the computation of parsimonious evolutionary scenarios, i.e. a shortest sequence of rearrangements transforming one arrangement of genes into another or the length of such a minimal scenario (Hannenhalli and Pevzner, 1995b; Sankoff, 1992; Watterson et al., 1982); the recons.
Computational Frameworks For Indel Aware Evolutionary Analysis Using Large Scale Genomic Sequence Data
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Author : Wei Wang
language : en
Publisher:
Release Date : 2021
Computational Frameworks For Indel Aware Evolutionary Analysis Using Large Scale Genomic Sequence Data written by Wei Wang and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021 with Electronic dissertations categories.
With the development of sequencing techniques, genetic sequencing data has been extensively used in evolutionary studies. The phylogenetic reconstruction problem, which is the reconstruction of evolutionary history from biomolecular sequences, is a fundamental problem. The evolutionary relationship between organisms is often represented by phylogeny, which is a tree or network representation. The most widely-used approach for reconstructing phylogenies from sequencing data involves two phases: multiple sequence alignment and phylogenetic reconstruction from the aligned sequences. As the amount of biomolecular sequence data increases, it has become a major challenge to develop efficient and accurate computational methods for phylogenetic analyses of large-scale sequencing data. Due to the complexity of the phylogenetic reconstruction problem in modern phylogenetic studies, the traditional sequence-based phylogenetic analysis methods involve many over-simplified assumptions. In this thesis, we describe our contribution in relaxing some of these over-simplified assumptions in the phylogenetic analysis.Insertion and deletion events, referred to as indels, carry much phylogenetic information but are often ignored in the reconstruction process of phylogenies. We take into account the indel uncertainties in multiple phylogenetic analyses by applying resampling and re-estimation. Another over-simplified assumption that we contributed to is adopted by many commonly used non-parametric algorithms for the resampling of biomolecular sequences, all sites in an MSA are evolved independently and identically distributed (i.i.d). Many evolution events, such as recombination and hybridization, may produce intra-sequence and functional dependence in biomolecular sequences that violate this assumption. We introduce SERES, a resampling algorithm for biomolecular sequences that can produce resampled replicates that preserve the intra-sequence dependence. We describe the application of the SERES resampling and re-estimation approach to two classical problems: the multiple sequence alignment support estimation and recombination-aware local genealogical inference. We show that these two statistical inference problems greatly benefit from the indel-aware resampling and re-estimation approach and the reservation of intra-sequence dependence.A major drawback of SERES is that it requires parameters to ensure the synchronization of random walks on unaligned sequences. We introduce RAWR, a non-parametric resampling method designed for phylogenetic tree support estimation that does not require extra parameters. We show that the RAWR-based resampling and re-estimation method produces comparable or typically better performance than the traditional bootstrap approach on the phylogenetic tree support estimation problem.We further relax the commonly used assumption of phylogeny. Evolutionary history is usually considered as a tree structure. Evolutionary events that cause reticulated gene flow are ignored. Previous studies show that alignment uncertainty greatly impacts downstream tree inference and learning. However, there is little discussion about the impact of MSA uncertainties on the phylogenetic network reconstruction. We show evidence that the errors introduced in MSA estimation decrease the accuracy of the inferred phylogenetic network, and an indel-aware reconstruction method is needed for phylogenetic network analysis.In this dissertation, we introduce our contribution to phylogenetic estimation using biomolecular sequence data involving complex evolutionary histories, such as sequence insertion and deletion processes and non-tree-like evolution.