This volume describes the foundations of phylogenomic analysis, bioinformatic resources, methodologies supporting the interface of genomic biology, and recent developments in phylogenomic analyses. Chapters guide readers through advances and challenges in the analysis of shallow and deep evolutionary processes with the retrodiction paradigm, analysis of viruses in pandemics, building a tree of life describing the organismal diversity of our planet, or mining k-mers or structural domains to understand the origin and evolution of proteins and proteomes. Written in the highly successful Methods in Molecular Biology series format, the chapters include brief introductions to the material, lists of necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and a Notes section which highlights tips on troubleshooting and avoiding known pitfalls.

Authoritative and cutting-edge, Evolutionary Genomics: Methods and Protocols aims to be comprehensive guide for **researchers in the field.

Inhalt

Retrodiction in Evolutionary Genomics A Philosophical Perspective.- Searching for Phylogenetic Networks.- Phylogenetic Placement using SCAMPP and Batch-SCAMPP.- Impact of Data Error on Phylogenetic Network Inferences from Gene Trees under the Multispecies Network Coalescent.- PhyloSystemX: Enhancing the Analysis of Interaction Networks.- Discovering, Genotyping, and Annotating Structural Variants with the Genome Analysis Toolkit (GATK).- Physics Determines and Evolution Shapes Basic Units of Protein Function and Allosteric Regulation.- Methods to Characterize Mutant Spectra of RNA Viruses. The Case of SARS-CoV-2.- Geographic and Temporal Dynamics of Viral Proteome Sequences.- Proteome-wide Ab Initio Structure Prediction of Evolving Viruses.- Phylogenomic Tree Reconstruction from Bacterial Genomes.- Feature Frequency Profile (FFP) Method: A Language Model for Whole-Genome( Organism ) Phylogeny.- Phylogeny Building for Structural Phylogenomic Research.- A Pipeline for Generating Datasets of 3-Dimensional Tertiary Interaction Characters for Model-Based Structural Phylogenetics.- MD-Phylogeny: Constructing Statistically Supported Phylogenetic Trees from Protein Structures using Molecular Dynamics.- Studying the Evolution of Protein Structure one Superfamily at a Time.- Protein Architecture Comparisons and the Reconstruction of the Last Universal Common Ancestor (LUCA).- Tracing the Origin and Evolution of the Secondary Structure of RNA.- Tracing Molecular Chronologies onto Growing Biological Networks.