Table of contents

  1. Front Matter
    Pages i-xvii
  2. Introduction: Bioinformatician’s Primers

    1. Front Matter
      Pages 1-1
    2. Noor Youssef, Aidan Budd, Joseph P. Bielawski
      Pages 3-31 Open Access
    3. Niko Beerenwinkel, Juliane Siebourg
      Pages 33-70 Open Access
    4. Stéphane Aris-Brosou, Nicolas Rodrigue
      Pages 71-117 Open Access
  3. Genomic Alignment and Homology Inference

    1. Front Matter
      Pages 119-119
    2. Colin N. Dewey
      Pages 121-147 Open Access
    3. Adrian M. Altenhoff, Natasha M. Glover, Christophe Dessimoz
      Pages 149-175 Open Access
    4. Wojciech Makałowski, Valer Gotea, Amit Pande, Izabela Makałowska
      Pages 177-207 Open Access
  4. Phylogenomics and Genome Evolution

    1. Front Matter
      Pages 209-209
    2. Liang Liu, Christian Anderson, Dennis Pearl, Scott V. Edwards
      Pages 211-239 Open Access
    3. Pere Puigbò, Yuri I. Wolf, Eugene V. Koonin
      Pages 241-269 Open Access
    4. Andrew K. Watson, Romain Lannes, Jananan S. Pathmanathan, Raphaël Méheust, Slim Karkar, Philippe Colson et al.
      Pages 271-308 Open Access
    5. Mario dos Reis, Ziheng Yang
      Pages 309-330 Open Access
    6. Sylvain Glémin, Clémentine M. François, Nicolas Galtier
      Pages 331-369 Open Access
  5. Natural Selection and Innovation in Genomic Sequences

    1. Front Matter
      Pages 371-371
    2. Carolin Kosiol, Maria Anisimova
      Pages 373-397 Open Access
    3. Christopher T. Jones, Edward Susko, Joseph P. Bielawski
      Pages 399-426 Open Access
    4. Stephanie J. Spielman, Steven Weaver, Stephen D. Shank, Brittany Rife Magalis, Michael Li, Sergei L. Kosakovsky Pond
      Pages 427-468 Open Access
    5. Sofia K. Forslund, Mateusz Kaduk, Erik L. L. Sonnhammer
      Pages 469-504 Open Access
  6. Population Genomics and Omics in Light of Disease and Evolution

    1. Front Matter
      Pages 531-531
    2. Søren Besenbacher, Thomas Mailund, Bjarni J. Vilhjálmsson, Mikkel H. Schierup
      Pages 533-553 Open Access
    3. Julien Y. Dutheil, Asger Hobolth
      Pages 555-589 Open Access
    4. Caner Bağcı, Sina Beier, Anna Górska, Daniel H. Huson
      Pages 591-604 Open Access
    5. Pjotr Prins, Geert Smant, Danny Arends, Megan K. Mulligan, Rob W. Williams, Ritsert C. Jansen
      Pages 635-652 Open Access
  7. Handling Genomic Data: Resources and Computation

    1. Front Matter
      Pages 653-653
    2. Ana Claudia Sima, Kurt Stockinger, Tarcisio Mendes de Farias, Manuel Gil
      Pages 655-690 Open Access
    3. Guy Baele, Daniel L. Ayres, Andrew Rambaut, Marc A. Suchard, Philippe Lemey
      Pages 691-722 Open Access
    4. Francesco Strozzi, Roel Janssen, Ricardo Wurmus, Michael R. Crusoe, George Githinji, Paolo Di Tommaso et al.
      Pages 723-745 Open Access
    5. Raoul J. P. Bonnal, Andrew Yates, Naohisa Goto, Laurent Gautier, Scooter Willis, Christopher Fields et al.
      Pages 747-766 Open Access
  8. Back Matter
    Pages 767-780

About this book


This open access book addresses the challenge of analyzing and understanding the evolutionary dynamics of complex biological systems at the genomic level, and elaborates on some promising strategies that would bring us closer to uncovering of the vital relationships between genotype and phenotype. After a few educational primers, the book continues with sections on sequence homology and alignment, phylogenetic methods to study genome evolution, methodologies for evaluating selective pressures on genomic sequences as well as genomic evolution in light of protein domain architecture and transposable elements, population genomics and other omics, and discussions of current bottlenecks in handling and analyzing genomic data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that lead to the best results. 

Authoritative and comprehensive, Evolutionary Genomics: Statistical and Computational Methods, Second Edition aims to serve both novices in biology with strong statistics and computational skills, and molecular biologists with a good grasp of standard mathematical concepts, in moving this important field of study forward.


Genome biology Genotype and phenotype Probability and statistics Sequence homology Molecular evolution Molecular data Open access

Editors and affiliations

  • Maria Anisimova
    • 1
  1. 1.Institute of Applied Simulations, School of Life Sciences and Facility ManagementZurich University of Applied Sciences (ZHAW)WädenswilSwitzerland

Bibliographic information

  • DOI
  • Copyright Information The Editor(s) (if applicable) and The Author(s) 2019
  • License CC BY
  • Publisher Name Humana, New York, NY
  • eBook Packages Springer Protocols
  • Print ISBN 978-1-4939-9073-3
  • Online ISBN 978-1-4939-9074-0
  • Series Print ISSN 1064-3745
  • Series Online ISSN 1940-6029
  • Buy this book on publisher's site