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Introduction to Computational Molecular Biology
João C. Setubal,João Meidanis +1 more
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This chapter discusses the construction of phylogenetic trees, a type of tree-building based on DNA assembly, and its applications in medicine, dentistry, and neuroscience.Abstract:
Preface 1. Basic Concepts of Molecular Biology 2. Strings, Graphs, and Algorithms 3. Sequence Comparison and Database Search 4. Fragment Assembly of DNA 5. Physical Mapping of DNA 6. Phylogenetic Trees 7. Genome Rearrangements 8. Molecular Structure Prediction 9. Epilogue: Computing with DNA Answers to Selected Exercises / References / Indexread more
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Data Mining: Concepts and Techniques
TL;DR: This book presents dozens of algorithms and implementation examples, all in pseudo-code and suitable for use in real-world, large-scale data mining projects, and provides a comprehensive, practical look at the concepts and techniques you need to get the most out of real business data.
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An Improved General Amino Acid Replacement Matrix
Si Quang Le,Olivier Gascuel +1 more
TL;DR: This method further refine this method by incorporating the variability of evolutionary rates across sites in the matrix estimation and using a much larger and diverse database than BRKALN, which was used to estimate WAG.
Data Mining: Concepts and Techniques (2nd edition)
Jiawei Han,Micheline Kamber +1 more
TL;DR: There have been many data mining books published in recent years, including Predictive Data Mining by Weiss and Indurkhya [WI98], Data Mining Solutions: Methods and Tools for Solving Real-World Problems by Westphal and Blaxton [WB98], Mastering Data Mining: The Art and Science of Customer Relationship Management by Berry and Linofi [BL99].
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Invitation to fixed-parameter algorithms
TL;DR: This paper discusses Fixed-Parameter Algorithms, Parameterized Complexity Theory, and Selected Case Studies, and some of the techniques used in this work.
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Applied cognitive task analysis (ACTA): a practitioner's toolkit for understanding cognitive task demands
TL;DR: A streamlined method of CTA, Applied Cognitive Task Analysis (ACTA), is presented, which consists of three interview methods that help the practitioner to extract information about the cognitive demands and skills required for a task.
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Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
Book
Computers and Intractability: A Guide to the Theory of NP-Completeness
TL;DR: The second edition of a quarterly column as discussed by the authors provides a continuing update to the list of problems (NP-complete and harder) presented by M. R. Garey and myself in our book "Computers and Intractability: A Guide to the Theory of NP-Completeness,” W. H. Freeman & Co., San Francisco, 1979.
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Introduction to Algorithms
TL;DR: The updated new edition of the classic Introduction to Algorithms is intended primarily for use in undergraduate or graduate courses in algorithms or data structures and presents a rich variety of algorithms and covers them in considerable depth while making their design and analysis accessible to all levels of readers.
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Molecular Evolutionary Genetics
TL;DR: Recent developments of statistical methods in molecular phylogenetics are reviewed and it is shown that the mathematical foundations of these methods are not well established, but computer simulations and empirical data indicate that currently used methods produce reasonably good phylogenetic trees when a sufficiently large number of nucleotides or amino acids are used.