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The book presents an overview and brief description of the most frequent methods of phylogenetic inference. It provides basic information on underlying assumptions of these methods, their advantages and disadvantages, and differences between them. The text is supposed to help readers to make informed decisions in choosing an optimal approach for solving a given problem and for a given type of data as well as in correct interpretation of results. The book begins with an overview of the types of data for phylogenetic analysis, databases and sequence alignment, followed by methods of parsimony, evolutionary models, distance methods, likelihood, Bayesian inference, testing hypotheses, and comparing phylogenies. A separate chapter is focused on phylogenetic methods based on morphological data. The final part deals with the theory of coalescent which is essential for an array of population genetic analyses including new approaches to phylogeography.

Cladistic analysis. --- Cladistic analysis --- Cladism --- Cladistic method --- Cladistic taxonomy --- Cladistics --- Cladograms --- Phylogenetic systematics --- Phylogenetic taxonomy --- Taxonomy, Cladistic --- Taxonomy, Phylogenetic --- Biology --- Branching processes --- Phylogeny --- Data processing. --- Classification

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"Nearly 300 clades - lineages of organisms - will be defined by reference to hypotheses of phylogenetic history rather than by taxonomic ranks and types. This volume will document the Real World uses of PhyloCode and will govern and apply to the names of clades, while species names will still be governed by traditional codes"--

Cladistic analysis. --- Phylogeny --- Nomenclature. --- Cladistic analysis --- Animal phylogeny --- Animals --- Phylogenetics --- Phylogeny (Zoology) --- Biology --- Evolution (Biology) --- Cladism --- Cladistic method --- Cladistic taxonomy --- Cladistics --- Cladograms --- Phylogenetic systematics --- Phylogenetic taxonomy --- Taxonomy, Cladistic --- Taxonomy, Phylogenetic --- Branching processes --- Nomenclature --- Classification --- Evolution. Phylogeny --- Animal systematics, taxonomy, nomencl.

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Systematics. Taxonomy. Nomenclature --- 57.065 --- 57.017 --- Cladistic analysis --- -Homology (Biology) --- Anatomy, Comparative --- Biology --- Evolution (Biology) --- Morphology --- Phylogeny --- Cladism --- Cladistic method --- Cladistic taxonomy --- Cladistics --- Cladograms --- Phylogenetic systematics --- Phylogenetic taxonomy --- Taxonomy, Cladistic --- Taxonomy, Phylogenetic --- Branching processes --- Phylogenetic classification systems --- Biological characteristics. Life histories --- Methodology --- Classification --- Homology (Biology). --- Methodology. --- homology --- phylogeny --- systematics --- 57.017 Biological characteristics. Life histories --- 57.065 Phylogenetic classification systems --- Homology (Biology)

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"The evolutionary history of species is traditionally represented using a rooted phylogenetic tree. However, when reticulate events such as hybridization, horizontal gene transfer or recombination are believed to be involved, phylogenetic networks that can accommodate non-treelike evolution have an important role to play. This book provides the first interdisciplinary overview of phylogenetic networks. Beginning with a concise introduction to both phylogenetic trees and phylogenetic networks, the fundamental concepts and results are then presented for both rooted and unrooted phylogenetic networks. Current approaches and algorithms available for computing phylogenetic networks from different types of datasets are then discussed, accompanied by examples of their application to real biological datasets. The book also summarises the algorithms used for drawing phylogenetic networks, along with the existing software for their computation and evaluation. All datasets, examples and other additional information and links are available from the book's companion website at www.phylogenetic-networks.org"-- "In the first part of this book we give an introduction to basic concepts from graph theory and systematics (Chapter 1). We briefly discuss the problem of aligning molecular sequences (Chapter 2) and give a more detailed introduction to the computation of phylogenetic trees from aligned sequences and distances (Chapter 3). Finally, we give a brief introduction to the computation of phyloge-netic networks, which also serves as an overview for the material presented in the second and third parts of the book (Chapter 4). Chapters 2 and 3 are provided for the sake of completeness and reference. They can be skipped by readers who have a basic knowledge of phylogenetic "--

Evolution. Phylogeny --- Cladistic analysis --- Phylogeny --- Data processing --- Mathematics --- Phylogeny. --- Data processing. --- Mathematics. --- Animal phylogeny --- Animals --- Phylogenetics --- Phylogeny (Zoology) --- Biology --- Evolution (Biology) --- Cladism --- Cladistic method --- Cladistic taxonomy --- Cladistics --- Cladograms --- Phylogenetic systematics --- Phylogenetic taxonomy --- Taxonomy, Cladistic --- Taxonomy, Phylogenetic --- Branching processes --- Classification --- Genetic Phenomena. --- Cladistic analysis - Data processing --- Cladistic analysis - Mathematics --- Genetic Phenomena --- Biological evolution

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Analyse cladistique --- Cladistic analysis --- Biogeography --- Biogeography. --- Cladistic analysis. --- Biogéographie --- Cladism --- Cladistic method --- Cladistic taxonomy --- Cladistics --- Cladograms --- Phylogenetic systematics --- Phylogenetic taxonomy --- Taxonomy, Cladistic --- Taxonomy, Phylogenetic --- Biology --- Branching processes --- Phylogeny --- Areography (Biology) --- Geographical distribution of animals and plants --- Species --- Species distribution --- Geography --- Classification --- Geographical distribution