Table of Contents

Overview
• Introduction
      • Mixing Colors
• Warnings Important notes
• Starting PyMood
• Quick Start
      • Project Scheme
      • Example Project Description
      • Project Implementation

PyMood BLAST Launcher
• Saving Your Sequence Files
• Input File Manipulation
      • Flip Fasta Header
      • Combine Files
      • Create Non-Redundant Dataset
• Advanced
      • Create Matrix From Ext. BLAST File
            • Create Annotation Files
      • Extract Seqs. from FASTA File (NCBI GI)
      • Extract Seqs. from Standard FASTA File
      • Split Sequences
      • Create HTML Pages from Info Files
      • Clustering
      • Sequence Processor
• PyMood BLAST Launcher Setup
      • FASTA Format
      • NCBI BLAST Setup Parameters
      • Select Query
      • Select Target
      • Output File
      • BLAST!
• PyMood BLAST Output
      • Files for the PyMood Pipeline
            • annotation Files
            • .matrix Files
            • .blast Files
      • Other Files
            • .all_hits Files
            • .info1 files
            • .info2 files
            • .blast_stat Files
            • Binary Files

PyMood (2D and 3D Viewers)
• PyMood Setup
      • PyMood Random Project
            • Canvas Options
            • Canvas Display
            • 2D Plot
            • Random Project Saving
            • 3D Plot
      • Data File Setup
            • rgb File Structure
      • Project from Data File
            • Canvas Options
            • Data File Import
• 2D Viewer
      • Canvas
      • 2D Plot
      • Data Saving and Generation of Web Pages
• 3D Viewer
      • Options
      • Moving, Rotating, Zooming
      • Selections
      • Annotation, Data Retrieval, and Saving
• Setting Up Custom RGB files
      • rgb File Structure
      • annotation File Structure

Misc
• Un-installation Instructions
• Libraries Used by PyMood / Copyright Info