Macclade

MacClade is a computer program for graphic and interactive analysis of phylogeny and character evolution for Apple Macintosh computers. It displays a cladogram and paints the branches to indicate reconstructed character evolution. The user can manipulate cladograms on screen as MacClade gives diagnostic feedback. Systematics and other evolutionary biologists can use its flexible and analytical tools to examine phylogenies or interpret character evolution in a phylogenetic context, yet its ease of use should allow students to grasp phylogenetic principles in an interactive environment. This is the user's manual.

"In this book, Andy Baxevanis and Francis Ouellette . . . haveundertaken the difficult task of organizing the knowledge in thisfield in a logical progression and presenting it in a digestibleform. And they have done an excellent job. This fine text will makea major impact on biological research and, in turn, on progress inbiomedicine. We are all in their debt." —Eric Lander from the Foreword Reviews from the First Edition "...provides a broad overview of the basic tools for sequenceanalysis ... For biologists approaching this subject for the firsttime, it will be a very useful handbook to keep on the shelf afterthe first reading, close to the computer." —Nature Structural Biology "...should be in the personal library of any biologist who usesthe Internet for the analysis of DNA and protein sequencedata." —Science "...a wonderful primer designed to navigate the novice throughthe intricacies of in scripto analysis ... The accomplished genesearcher will also find this book a useful addition to theirlibrary ... an excellent reference to the principles ofbioinformatics." —Trends in Biochemical Sciences This new edition of the highly successful Bioinformatics:A Practical Guide to the Analysis of Genes and Proteinsprovides a sound foundation of basic concepts, with practicaldiscussions and comparisons of both computational tools anddatabases relevant to biological research. Equipping biologists with the modern tools necessary to solvepractical problems in sequence data analysis, the Second Editioncovers the broad spectrum of topics in bioinformatics, ranging fromInternet concepts to predictive algorithms used on sequence,structure, and expression data. With chapters written by experts inthe field, this up-to-date reference thoroughly covers vitalconcepts and is appropriate for both the novice and the experiencedpractitioner. Written in clear, simple language, the book isaccessible to users without an advanced mathematical or computerscience background. This new edition includes: All new end-of-chapter Web resources, bibliographies, andproblem sets Accompanying Web site containing the answers to the problems,as well as links to relevant Web resources New coverage of comparative genomics, large-scale genomeanalysis, sequence assembly, and expressed sequence tags A glossary of commonly used terms in bioinformatics andgenomics Bioinformatics: A Practical Guide to the Analysis of Genesand Proteins, Second Edition is essential reading forresearchers, instructors, and students of all levels in molecularbiology and bioinformatics, as well as for investigators involvedin genomics, positional cloning, clinical research, andcomputational biology.

Bioinformatics is an upcoming discipline of Life Sciences. It is an integration of computer science, and mathematical and statistical methods to manage and analyze the biological data. The fundamental issues that directly impact an understanding of life at structural, functional and molecular level, and regulation of gene expression can be studied by using bioinformatics tools. The Fundamentals of Bioinformatics is a comprehensive book for undergraduates, postgraduates and research scholars, who urge to learn about theoretical as well as practical aspects of this upcoming field. This pioneering book provides up-to-date information on bioinformatics and emphasizes recent topics like drug design technology, pharmacogenomics, proteomics and genomics. The present textbook will be an asset to Life sciences and technology institutions, since it has been designed based on the prescribed syllabus of various Indian Universities and aboard, and cover all the important topics on Bioinformatics.

The application of molecular techniques is rapidly transforming the study of plant systematics. The precision they offer enables researchers to classify plants that have not been subject to rigorous classification before and thus allows them to obtain a clearer picture of evolutionary relationships. Plant Molecular Systematics is arranged both conceptually and phylogenetically to accommodate the interests not only of general systematists, but also those of people interested in a particular plant family. The first part discusses molecular sequencing; the second reviews restriction site analysis and the sequencing of mitochondrial DNA. A third section details the analysis of ribosomal DNA and chloroplast DNA. The following section introduces model studies involving well-studied families such as the Onagraceae, Compositae and Leguminosae. The book concludes with a section addressing theoretical topics such as data analysis and the question of morphological vs. molecular data.

Plant Systematics is a comprehensive and beautifully illustrated text, covering the most up-to-date and essential paradigms, concepts, and terms required for a basic understanding of plant systematics. This book contains numerous cladograms that illustrate the evolutionary relationships of major plant groups, with an emphasis on the adaptive significance of major evolutionary novelties. It provides descriptions and classifications of major groups of angiosperms, including over 90 flowering plant families; a comprehensive glossary of plant morphological terms, as well as appendices on botanical illustration and plant descriptions. Pedagogy includes review questions, exercises, and references that complement each chapter. This text is ideal for graduate and undergraduate students in botany, plant taxonomy, plant systematics, plant pathology, ecology as well as faculty and researchers in any of the plant sciences. * The Henry Allan Gleason Award of The New York Botanical Garden, awarded for "Outstanding recent publication in the field of plant taxonomy, plant ecology, or plant geography" (2006) * Contains numerous cladograms that illustrate the evolutionary relationships of major plant groups, with an emphasis on the adaptive significance of major evolutionary novelties *Provides descriptions and classifications of major groups of angiosperms, including over 90 flowering plant families * Includes a comprehensive glossary of plant morphological terms as well as appendices on botanical illustration and plant description

Laboratory Protocols in Fungal Biology presents the latest techniques in fungal biology. This book analyzes information derived through real experiments, and focuses on cutting edge techniques in the field. The book comprises 57 chapters contributed from internationally recognised scientists and researchers. Experts in the field have provided up-to-date protocols covering a range of frequently used methods in fungal biology. Almost all important methods available in the area of fungal biology viz. taxonomic keys in fungi; histopathological and microscopy techniques; proteomics methods; genomics methods; industrial applications and related techniques; and bioinformatics tools in fungi are covered and complied in one book. Chapters include introductions to their respective topics, list of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting. Each chapter is self-contained and written in a style that enables the reader to progress from elementary concepts to advanced research techniques. Laboratory Protocols in Fungal Biology is a valuable tool for both beginner research workers and experienced professionals. Coming Soon in the Fungal Biology series: Goyal, Manoharachary / Future Challenges in Crop Protection Against Fungal Pathogens Martín, García-Estrada, Zeilinger / Biosynthesis and Molecular Genetics of Fungal Secondary Metabolites Zeilinger, Martín, García-Estrada / Biosynthesis and Molecular Genetics of Fungal Secondary Metabolites, Volume 2 van den Berg, Maruthachalam / Genetic Transformation Systems in Fungi Schmoll, Dattenbock / Gene Expression Systems in Fungi Dahms / Advanced Microscopy in Mycology

Amniote Origins integrates modern systematic methods with studies of functional and physiological processes, and illustrates how studies of paleobiology can be illuminated by studies of neonatology. For this reason, comparative anatomists and physiologists, functional morphologists, zoologists, and paleontologists will all find this unique volume very useful. Inspired by the prospect of integrating fields that have long been isolated from one another, Amniote Origins provides a thorough and interdisciplinary synthesis of one of the classic transitions of evolutionary history. Integrates modern systematic methods with studies of functional and physiological processes Illustrates how studies of paleobiology can be illuminated by studies of neonatology Provides a thorough and interdisciplinary synthesis of one of the classic transitions of evolutionary history

Bioinformatics for Beginners: Genes, Genomes, Molecular Evolution, Databases and Analytical Tools provides a coherent and friendly treatment of bioinformatics for any student or scientist within biology who has not routinely performed bioinformatic analysis. The book discusses the relevant principles needed to understand the theoretical underpinnings of bioinformatic analysis and demonstrates, with examples, targeted analysis using freely available web-based software and publicly available databases. Eschewing non-essential information, the work focuses on principles and hands-on analysis, also pointing to further study options. Avoids non-essential coverage, yet fully describes the field for beginners Explains the molecular basis of evolution to place bioinformatic analysis in biological context Provides useful links to the vast resource of publicly available bioinformatic databases and analysis tools Contains over 100 figures that aid in concept discovery and illustration