Bioinformatics: Volume I: Data, Sequence Analysis, and Evolution

Preface...
Table of Contents...
Contributing Authors...

Part I Data and Databases

1. Genome Sequencing
Mansi Verma, Samarth Kulshreshtha, and Ayush Puri

2. Sequence Assembly
Xiaoqiu Huang

3. A Practical Approach to Protein Crystallography
Andrea Ilari and Carmelinda Savino

4. Managing Sequence Data
Christopher O'Sullivan, Benjamin Busby, and Ilene Karsch Mizrachi

5. Genome Annotation
Imad Abugessaisa, Takeya Kasukawa, and Hideya Kawaji

6. Working with Ontologies
Frank Kramer and Tim Bei barth

7. The Classification of Protein Domains
Natalie L. Dawson, Ian Sillitoe, Russell L. Marsden, and Christine A. Orengo

Part II Sequence Analysis

8. Multiple Sequence Alignment
Punto Bawono, Maurits Dijkstra, Walter Pirovano, Anton Feenstra, Sanne Abeln, and Jaap Heringa

9. Large-Scale Sequence Comparison
Devi Lal and Mansi Verma

10. Genomic Database Searching
James R. A. Hutchins

11. Finding Genes in Genome Sequence
Alice Carolyn McHardy and Andreas Kloetgen

12. Sequence Segmentation with changeptGUI
Edward Tasker and Jonathan M. Keith

Part III Phylogenetics and Evolution

13. Measuring Natural Selection
Anders Gon?alves da Silva

14. Inferring Trees
Simon Whelan and David A. Morrison

15. Identifying Optimal Models of Evolution
Lars S. Jermiin, Vivek Jayaswal, Faisal M. Ababneh, and John Robinson

16. Scaling Up the Phylogenetic Detection of Lateral Gene Transfer Events
Cheong Xin Chan, Robert G. Beiko, and Mark A. Ragan

17. Detecting and Analyzing Genetic Recombination Using RDP4
Darren P. Martin, Ben Murrell, Arjun Khoosal, and Brejnev Muhire

18. Species Tree Estimation from Genome-Wide Data with Guenomu
Leonardo de Oliveira Martins and David Posada