Chapter 5. File Formats

Table of Contents

5.1. Introduction
5.2. Introduction to Sequence Formats
5.2.1. What is a Sequence Format?
5.2.2. Supported Sequence Formats
5.2.3. Contents of a Sequence Entry Identification Bibliographic Information Annotation and Features The Sequence
5.2.4. Specifying Sequences on the Command Line
5.2.5. Applications for Basic Sequence Manipulation
5.3. Introduction to Feature Formats
5.3.1. What is a Feature?
5.3.2. Supported Feature Formats
5.3.3. How are Features Stored ?
5.3.4. Applications for Features
5.3.5. Specifying Features on the Command line
5.4. Introduction to Alignment Formats
5.4.1. What is an Alignment Format?
5.4.2. Supported Alignment Formats
5.4.3. Contents of an Alignment File
5.4.4. Specifying Alignments on the Command Line
5.4.5. Applications for Sequence Alignment
5.5. Introduction to Report Formats
5.5.1. What is a Report Format?
5.5.2. Supported Report Formats
5.5.3. Inside a Report
5.5.4. Specifying Reports on the Command line
5.5.5. Applications that use Reports