Editing the alignment

This chapter explains how to work efficiently with UGENE Alignment Editor. You will learn how to modify the alignment, remove all kind of gaps, align sequences automatically, copy and paste regions, add new sequences and create sub alignments. The chapter includes the following sections:

Basics

• Undo/redo framework

• Selection mode

• Remove gaps

Aligning sequences

Working with sequence list

• Add new sequences

• Copy sequences

• Sort sequences

Create sub-alignment

Basics

Undo/redo framework

The editor tracks all modifications of the aligned sequences.
When a modification happens the current state of the multiple sequence alignment object is being recorded.

You can apply any previous state and redo the modifications using corresponding buttons on the toolbar:

Selection mode

While in the Sequence area, if you hold left mouse button and move the cursor, you will activate selection mode. By moving the cursor you can adjust the size of the selection.
Releasing the mouse button will result in exiting the selection mode.

Using the selection mechanism you can remove selected regions from the aligned sequences by using context menu item Edit->Remove selection or simply by pressing Del key within the Sequence area.

Selection mode is available in the Sequence name list and Consensus area too. The difference between these areas and Sequence area is that here you can add to selection whole rows or columns respectively.

Hint: To cancel the selection press Esc.

Remove gaps

There are several options to remove gaps:

Remove all gaps This action will eliminate all gaps from the alinged sequences.

Delete column with gaps The gaps will be deleted only if they form a column with the height equal to height of the alignment.

These options are available from context menu or from main menu item Actions in the submenu Edit:

Aligning sequences

UGENE alignment editor integrates several popular multiple sequence alignment algorithms.
Below is the list of available algorithms and links to the documentation:

• Port of popular algorithm MUSCLE 3 .
• KAlign plugin: effective work with huge alighments
• MUSCLE 4: preview version of recent algorithm version

To align sequences activate context menu using right mouse button or main menu item Actions and choose prefered alignment method.

Also check out our video tutorials devoted to multiple sequence alignment:

• Making a multiple sequence alignment from FASTA file
• Working with large alignments in UGENE
• Performing profile-to-profile and profile-to-sequence MUSCLE alignments
• Running remote MUSCLE task

The podcasts are available at Unipro UGENE YouTube channel.

Working with sequence list

Adding new sequences

You can add new sequences to the alignment using context submenu Add.

There are two ways to add new sequence to current alignment:

• From the file in compatible format (FASTA, GenBank etc.). List of support data formats can be found here.

• From the current project.
  If you activate this item, the following dialog will appear:
  
  You will see Project Tree View filtered to show only appropriate sequences. Select the items to add and press OK.

Copy sequences

To copy current selection use context menu or main menu item Actions and click Copy->Copy selection. The hotkey for this action is Ctrl+X.

To copy one or several sequences do the following:

• Select the sequences in the Sequence list area;
• Use "Copy selection" menu item in the Sequence area or use hot key combination. Note that if you activate context menu in Sequence list area you will lose you current selection.

To copy consensus sequence use context menu item Copy->Copy consensus

Sort sequences

To sort sequences by name in the alphabetical order activate context menu (right mouse button) and choose item View->Sort sequences by name.

Create subalignment

With Alignment Editor you can easily create sub-alignment from existing alignment.
To perform this operation activate context menu and execute action Edit->Create sub-alignment.

The following dialog will appear:

By default currently selected region will be used as subalignment region. You can change this region by changing subalignment start and end positon and modifying Selected sequences list.

It is required to set the filename for the subaligment file in the field Path.

Optionally you can add the newly created subalignment to the project by checking the corresponding box.

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