Mathematics of evolution and phylogeny /
| Other Authors: | |
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| Format: | Book |
| Language: | English |
| Published: |
Oxford ; New York :
Oxford University Press,
2005.
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| Subjects: | |
| Online Access: | http://search.ebscohost.com/login.aspx?direct=true&scope=site&db=nlebk&AN=191256 |
Table of Contents:
- 6 Hadamard conjugation: an analytic tool for phylogenetics
- 6.1 Introduction
- 6.2 Hadamard conjugation for two sequences
- 6.2.1 Hadamard matrices-a brief introduction
- 6.3 Some symmetric models of nucleotide substitution
- 6.3.1 Kimura's 3-substitution types model
- 6.3.2 Other symmetric models
- 6.4 Hadamard conjugation-Neyman model
- 6.4.1 Neyman model on three sequences
- 6.4.2 Neyman model on four sequences
- 6.4.3 Neyman model on n + 1 sequences
- 6.5 Applications: using the Neyman model
- 6.5.1 Rate variation
- 6.5.2 Invertibility
- 6.5.3 Invariants
- 6.5.4 Closest tree
- 6.5.5 Maximum parsimony
- 6.5.6 Parsimony inconsistency, Felsenstein's example
- 6.5.7 Parsimony inconsistency, molecular clock
- 6.5.8 Maximum likelihood under the Neyman model
- 6.6 Kimura's 3-substitution types model
- 6.6.1 One edge
- 6.6.2 K3ST for n + 1 sequences.; 6.7 Other applications and perspectives
- 7 Phylogenetic networks
- 7.1 Introduction
- 7.2 Median networks
- 7.3 Visual complexity of median networks
- 7.4 Consensus networks
- 7.5 Treelikeness
- 7.6 Deriving phylogenetic networks from distances
- 7.7 Neighbour-net
- 7.8 Discussion
- Acknowledgements
- 8 Reconstructing the duplication history of tandemly repeated sequences
- 8.1 Introduction
- 8.2 Repeated sequences and duplication model
- 8.2.1 Di.erent categories of repeated sequences
- 8.2.2 Biological model and assumptions
- 8.2.3 Duplication events, duplication histories, and duplication trees
- 8.2.4 The human T-cell receptor Gamma genes
- 8.2.5 Other data sets, applicability of the model
- 8.3 Mathematical model and properties
- 8.3.1 Notation
- 8.3.2 Root position
- 8.3.3 Recursive de.nition of rooted and unrooted duplication trees
- 8.3.4 From phylogenies with ordered leaves to duplication trees.; 8.3.5 Topñdown approach and leftñright properties of rooted duplication trees
- 8.3.6 Counting duplication histories
- 8.3.7 Counting simple event duplication trees
- 8.3.8 Counting (unrestricted) duplication trees
- 8.4 Inferring duplication trees from sequence data
- 8.4.1 Preamble
- 8.4.2 Computational hardness of duplication tree inference
- 8.4.3 Distance-based inference of simple event duplication trees
- 8.4.4 A simple parsimony heuristic to infer unrestricted duplication trees
- 8.4.5 Simple distance-based heuristic to infer unrestricted duplication trees
- 8.5 Simulation comparison and prospects
- Acknowledgements
- 9 Conserved segment statistics and rearrangement inferences in comparative genomics
- 9.1 Introduction
- 9.2 Genetic (recombinational) distance
- 9.3 Gene counts
- 9.4 The inference problem
- 9.5 What can we infer from conserved segments?
- 9.6 Rearrangement algorithms
- 9.7 Loss of signal
- 9.8 From gene order to genomic sequence.; 9.8.1 The Pevzner-Tesler approach
- 9.8.2 The re-use statistic r
- 9.8.3 Simulating rearrangement inference with a block-size threshold
- 9.8.4 A model for breakpoint re-use
- 9.8.5 A measure of noise?
- 9.9 Between the blocks
- 9.9.1 Fragments
- 9.10 Conclusions
- Acknowledgements
- 10 The inversion distance problem
- 10.1 Introduction and biological background
- 10.2 De.nitions and examples
- 10.3 Anatomy of a signed permutation
- 10.3.1 Elementary intervals and cycles
- 10.3.2 E.ects of an inversion on elementary intervals and cycles
- 10.3.3 Components
- 10.3.4 Effects of an inversion on components
- 10.4 The HannenhalliñPevzner duality theorem
- 10.4.1 Sorting oriented components
- 10.4.2 Computing the inversion distance
- 10.5 Algorithms
- 10.6 Conclusion
- Glossary
- 11 Genome rearrangements with gene families
- 11.1 Introduction
- 11.2 The formal representation of the genome
- 11.3 Genome rearrangement
- 11.4 Multigene families.; 11.5 Algorithms and models
- 11.5.1 Exemplar distance
- 11.5.2 Phylogenetic analysis
- 11.6 Genome duplication
- 11.6.1 Formalizing the problem
- 11.6.2 Methodology
- 11.6.3 Analysing the yeast genome
- 11.6.4 An application on a circular genome
- 11.7 Duplication of chromosomal segments
- 11.7.1 Formalizing the problem
- 11.7.2 Recovering an ancestor of a semi-ambiguous genome
- 11.7.3 Recovering an ancestor of an ambiguous genome
- 11.7.4 Recovering the ancestral nodes of a species tree
- 11.8 Conclusion.