Coloring methods in Multiple Alignment View

Introduction

This tutorial will serve as a consolidation space for all existing help on Coloring methods in Multiple Sequence Alignment View.

Step 1: Download example file

Download example file

Step 2: Open Multiple Sequence View

Open the example file (Open - File Import). Set the File Format drop-down to "Text Alignment files".

Click Next twice, then Finish, leaving the default settings. New project will be added to your workspace.

Right-click the new project and select Open New View command. New View menu will be displayed.

Click on the Multiple Alignment View. Multiple Alignment view will be displayed.

Step 3: Explore Coloring methods

Select your region of interest an zoom to sequence.

Right-click anywhere in your region of interest and select Coloration - Select Method from the context menu.

Alignment Scoring Methods menu will be displayed.

Explore the following available scoring methods (described in detail in the Multiple Sequence Alignment Viewer documentation):

• BLOSUM
• Show Differences
• Frequency-based Difference
• Hydropathy Scale
• Membrane Preference
• Rasmol Amino Acid Colors
• Shapely Amino Acid Colors
• Signal sequence
• Size
• Conservation