Evolutionary genomics : methods and protocols / edited by Gustavo Caetano-Anollés

Format:

Book

Contributor:

Caetano-Anollés, Gustavo, 1955- editor.

Series:

Methods in molecular biology ; v. 2981.

Methods in molecular biology, 1940-6029 ; 2981

Language:

English

Subjects (All):

Evolutionary genetics.

Genomics.

Medical Subjects:

Genomics.

Physical Description:

1 online resource

Place of Publication:

New York, NY : Humana Press, [2026]

Summary:

"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"-- Springer Nature Link

Contents:

Retrodiction in evolutionary genomics : a philosophical perspective / Elliott Sober

Searching for phylogenetic networks / Ward C. Wheeler

Phylogenetic placement using SCAMPP and Batch-SCAMPP / Eleanor Wedell, Chengze Shen and Tandy Warnow

Impact of data error on phylogenetic network inference from gene trees under the multispecies network coalescent / Mehrdad Tamiji, Nicolae Sapoval and Luay Nakhleh

PhyloSystemX : enhancing the analysis of interaction networks / Hugo Bonnefous, Yu Zhang, Philippe Lopez, François-Joseph Lapointe and Eric Bapteste

Discovering, genotyping, and annotating structural variants with the genome analysis toolkit (GATK) / Derek Caetano-Anollés

Physics determines and evolution shapes basic units of protein function and allosteric regulation / Igor N. Berezovsky

Methods to characterize mutant spectra of RNA viruses : the case of SARS-CoV-2 / Celia Perales, María Eugenia Soria, Ana Isabel de Ávila, Brenda Martínez-González, Isabel Gallego, Carlos García-Crespo, Pilar Somovilla, Pablo Mínguez, Ignacio Gadea and Esteban Domingo

Geographic and temporal dynamics of viral proteome sequences / Tre Tomaszewski

Proteome-wide ab initio structural analysis of viral evolution / Muhammad Asif Ali and Gustavo Caetano-Anollés

Phylogenomic tree reconstruction from bacterial genomes / Kyung Mo Kim and Kyuin Hwang

Feature frequency profile (FFP) method : a language model for whole-genome (“organism”) phylogeny / JaeJin Choi, Byung-Ju Kim and Sung-Hou Kim

Phylogeny building for structural phylogenomic research / Arshan Nasir and Gustavo Caetano-Anollés

A pipeline for generating datasets of three-dimensional tertiary interaction characters for model-based structural phylogenetics / Nicholas J. Matzke, Caroline Puente Lelievre and Matthew A. B. Baker

MD-phylogeny : constructing statistically supported phylogenetic trees from protein structures using molecular dynamics / Désirée B. Langer, Ashar J. Malik, Paul Klemm, Jane R. Allison and Anthony M. Poole

Studying the evolution of protein structure one superfamily at a time / Adrián Cruz-González, Ricardo Hernández-Morales, José Alberto Campillo-Balderas and Rodrigo Jácome

Protein architecture comparisons and the reconstruction of the last universal common ancestor (LUCA) / Ricardo Hernández-Morales, Coral C. G. Luna, Antonio Lazcano and Arturo Becerra

Tracing the origin and evolution of the secondary structure of RNA / Fengjie Sun and Gustavo Caetano-Anollés

Tracing molecular chronologies onto growing biological networks / M. Fayez Aziz and Gustavo Caetano-Anollés

Notes:

Includes bibliographical references and index

Online resource; title from PDF title page (Springer Nature Link, viewed May 21, 2026)

Other Format:

Print version: Evolutionary genomics

ISBN:

9781071648360

1071648365

OCLC:

1579000792

Publisher Number:

CIPO000350275

Access Restriction:

Restricted for use by site license