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