TAILIEUCHUNG - The Phylogenetic Handbook

The idea for The Phylogenetic Handbook was conceived during an early edition of theWorkshop on Virus Evolution andMolecular Epidemiology. The rationale was simple: to collect the information being taught in the workshop and turn it into a comprehensive, yet simply written textbook with a strong practical component. Marco and Annemie took up this challenge, and, with the help of many experts in the field, successfully produced the First Edition in 2003. The resulting text was an excellent primer for anyone taking their first computational steps into evolutionary biology, and, on a personal note, inspired me to try out many of the techniques introduced by the book in my. | A Practical Approach to Hypothecs Testing Second Edition CAUItllM Phylogenetic Handbook Edited by Philippe MAKOSalcmiand Annc-MKkc Vandammc Cambridge g 9 780521877107 This page intentionally left blank The Phylogenetic Handbook Second Edition The Phylogenetic Handbook provides a comprehensive introduction to theory and practice of nucleotide and protein phylogenetic analysis. This second edition includes seven new chapters covering topics such as Bayesian inference tree topology testing and the impact of recombination on phylogenies. The book has a stronger focus on hypothesis testing than the previous edition with more extensive discussions on recombination analysis detecting molecular adaptation and genealogy-based population genetics. Many chapters include elaborate practical sections which have been updated to introduce the reader to the most recent versions of sequence analysis and phylogeny software including Blast FastA Clustal T-coffee Muscle Dambe Tree-Puzzle Phylip Mega4 Paup Iqpnni Consel ModelTest ProtTest Paml HyPhy MrBayes Beast Lamarc SplitsTree and Rdp3. Many analysis tools are described by their original authors resulting in clear explanations that constitute an ideal teaching guide for advanced-level undergraduate and graduate students. Philippe Lemey is a FWO postdoctoral researcher at the Rega Institute Katholieke Universiteit Leuven Belgium where he completedhis . in Medical Sciences. He has been an EMBO Fellow and a Marie-Curie Fellow in the Evolutionary Biology Group at the Department of Zoology University of Oxford. His research focuses on molecular evolution of viruses by integrating molecular biology and computational approaches. Marco Salemi is Assistant Professor at the Department of Pathology Immunology and Laboratory Medicine of the University of Florida School of Medicine Gainesville USA. His research interests include molecular epidemiology intra-host virus evolution and the application of phylogenetic and .

• Y học thường thức
• Phylogenetic inference
• Theory
• Multiple sequence alignment
• Data preparation
• molecular evolution
• database searching
• Sequence databases
• BMC Bioinformatics
• Bayesian inference
• Conventional phylogenetic
• Phylogenetic estimates
• Similar estimates
• Phylogenetic network
• Large scale
• Incomplete lineage sorting
• Gene flow
• Genome Biology
• Ortholog inference
• Gene tree inference
• Gene duplication
• Comparative genomics
• Gene trees
• Species trees
• DNA barcodes
• ITS rDNA gene
• Tacca chantrieri
• Phylogenetic tree
• Genus Tacca
• Journal of Botany
• Mexican clade
• Mitochondrial DNA (CoxIII)
• Phylogenetic perspective
• Fragment amplification
• Evolutionary history
• Gene family
• Nucleotide Substitution
• Bayesian Networks
• Statistical Inference
• Bayesian Network
• Learning Paradigm
• Long branch attraction
• Lineage rate heterogeneity
• Phylogenetic methods
• Sequence subsampling
• Alignment free methods
• Sequence comparison
• Phylogeny reconstruction
• Average common substring
• Biological knowledge
• Character matrices
• Selecting informative subsets
• Sparse supermatrices increases
• Tree inference
• Heterogeneous phylogenetic signal
• Distance methods
• Reconstruct evolutionary history
• Bioinformatic pipelines
• Plant Biology
• Sucrose metabolism
• Gene expression
• Non photosynthetic tissues
• BMC Genomics
• Bixa orellana
• Next generation sequencing
• Center for Veterinary Medicine
• Instituto de Medicina Tradicional
• Phylogenetic reconstruction
• Quartet plurality
• Horizontal gene transfer
• Supertree reconstruction
• Prokaryotic evolution
• Journal of Zoology
• Phylogenetic analysis
• Mitochondrial cytochrome oxidase I gene
• Maximum likelihood
• Non colinear
• Genome alignment
• Multiple genome alignment
• Single cell
• Lineage tracing
• Rapid growth
• Phylogenetic relationships