Program Tnt
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Refining Phylogenetic Analyses
This volume discusses the aspects of a phylogenetic analysis that go beyond basic calculation of most parsimonious trees. Practical application of all principles discussed is illustrated by reference to TNT, a freely available software package that can perform all the steps needed in a phylogenetic analysis. The first problem considered is how to summarize and compare multiple trees (including identification and handling wildcard taxa). Evaluation of the strength of support for groups, another critical component of any phylogenetic analysis, is given careful consideration. The different interpretations of measures of support are discussed and connected with alternative implementations. The book reviews rationales for estimating character reliability on the basis of homoplasy, with particular attention to morphological characters. The main methods for character weighting and their practical implementation, several of them unique to TNT, are discussed ad libitum. Also unique to TNT is the ability to directly analyze morphometric data (including landmarks), on the same footing as discrete characters. Finally, the scripting language of TNT is introduced. With scripting, it is possible to "program" TNT to create personalized routines and automate complex calculations, taking analyses to the next level and allowing exploration of new methods and ideas. Key Features Discusses the treatment of ambiguity in phylogenetic analyses in depth, for summarizing results or comparing trees Reviews literature on arguments and methods for weighting morphological characters and their practical application Describes theory and application of methods for evaluating strength of group support, based on either resampling or comparisons with suboptimal trees Discusses the use of morphometric characters in phylogenetic analysis Presents extensive information on commands and options of the TNT computer program, including the use and creation of scripts
Mathematics in Programming
The book presents the mathematical view and tools of computer programming with broad and friendly context. It explains the basic concepts such as recursion, computation model, types, data, and etc. The book serves as an introductory and reference guide to the engineers, students, researchers, and professionals who are interested in functional programming, type system, and computer programming languages. The book covers seven topics. Firstly, it lays out the number system based on Peano Axioms and demonstrates the isomorphic computer data structures. Then, it introduces Lambda calculus as a computing model and recursion, an important programming structure, with the Y-combinator. It next presents the basic abstract algebra, including group and fields, and provides a friendly introduction to Galois theory. After that, it uses category theory as a tool to explain several concepts in computer programming, including the type system, polymorphism, null handler, and recursive data types, then followed by an application of program optimization. In the last two chapters, the author shows how to program with the concept of infinity through stream and lazy evaluation, and then explains the naïve set theory and transfinite numbers, from which the logic paradox arises. Finally, it introduces four historical views of mathematical foundation, as well as Gödel’s incompleteness theorems developed in 1930s, and how they define the boundaries of computer programming. Additionally, the book provides biographies, stories, and anecdotes of 25 mathematicians, along with over 130 exercises and their corresponding answers.
International Tables for Crystallography, Volume F
International Tables for Crystallography Volume F is an expert guide to macromolecular crystallography for the structural biologist. It was commissioned by the International Union of Crystallography in recognition of the extraordinary contributions that knowledge of macromolecular structure has made, and will make, to the analysis of biological systems, from enzyme catalysis to the workings of a whole cell. The volume covers all stages of a crystallographic analysis from the preparation of recombinant proteins, through crystallization, diffraction data collection, phase determination, structure validation and structure analysis. Although the volume is written for experienced scientists, it is recognized that the reader is more likely to be a biologist interested in structure than a classical crystallographer interested in biology. Thus, there are chapters on the fundamentals, history and current perspectives of macromolecular crystallography, as well as on useful programs and databases such as the Protein Data Bank. Each chapter is written by one or more internationally recognized experts. This second edition features 19 new articles and many articles from the first edition have been revised. The new articles cover topics such as standard definitions for quality indicators, expression of membrane proteins, protein engineering, high-throughput crystallography, radiation damage, merohedral twinning, low-resolution ab initio phasing, robotic crystal loading, whole-cell X-ray diffraction imaging and halogen interactions in biological crystal structures. There are also new articles on relevant software, including software for electron microscopy. These enhancements will ensure that Volume F continues to be a key reference for macromolecular crystallographers and structural biologists. More information on the series can be found at: http://it.iucr.org