ABSTRACT
SECTION 1 MULTIPLE SEQUENCE ALIGNMENTS 82 Part I Introduction 82
1. Why Are Multiple Sequence Alignments Needed? 82 2. What Is Involved in Multiple Sequence Alignments? 83 3. New Development in Multiple Sequence Alignment Programs 86
Part II Step-By-Step Tutorial 87 1. Align Multiple Protein Sequences 87 2. Edit and Publish Aligned Multiple Protein Sequences 90
Part III Sample Data 92 1. Human PBEF Amino Acid Sequence in the FASTA Format 92 2. Mouse PBEF Amino Acid Sequence in the FASTA Format 92 3. Rat PBEF Amino Acid Sequence in the FASTA Format 93
SECTION 2 BUILDING A PHYLOGENETIC TREE 93 Part I Introduction 93
1. What Is Phylogenetics? 93 2. Why Is Phylogenetic Analysis Needed? 93 3. What Activities Are Involved in Phylogenetic Analyses? 94 4. New Developments in Phylogenetic Analyses 96
Part II Step-By-Step Tutorial 97 1. Collecting a Set of Homologous Protein Sequences 98 2. Multiple Sequence Alignments 99
3. Building the Phylogenetic Tree 100 4. Tree Evaluation 101 5. Tree Visualization 101
Part III Sample Data (Partial Listing) 103
Phylogenetics is the field of biology that deals with identifying and understanding the relationships between the many different kinds of life on earth. In the past, phylogenetic analysis was heavily based on morphological data. With the sequencing of the human genome now complete and a number of other animal and plant genome sequences on the horizon, well-resolved molecular trees based on molecular data (nuclear DNA and derived protein data) have become an important tool in phylogenetical analysis. Molecular trees can serve as scaffolds for investigating evolutionary relationships. We are inching closer to understanding the organization and structure of the ancestral mammalian and plant genome, as well as the differences that make each species unique. This chapter commences with multiple sequence alignments in Section 1 and then introduces phylogenetical analysis in Section 2. In line with the format and style throughout this book, each section starts with a theoretical introduction in Part I, continues with a step-by-step tutorial in Part II, and ends with the presentation of sample data in Part III.
