Multiple sequence alignment (MSA Editor).  If you open a multiple sequence alignment, for example ugene/data/samples/CLUSTALW/COI.aln, Alignment Editor appears. The following views are available: the project view with your documents, the Alignment Editor with your alignment, options panel with additional info and algorithms:

<center>
  <img src="/wiki/download/attachments/2883700/msa.png"/>
</center>

Alignment Editor - an object view used to visualize and edit DNA, RNA or protein multiple sequence alignments.

You can also use algorithms and instruments from the context menu or the toolbar: 

<center>
  <img src="/wiki/download/attachments/2523429/pic5.png"/>
</center>

Example 2:Build a tree from your alignment. You can do this by three different ways:

a. From the toolbar:

<center>
  <img src="/wiki/download/attachments/2523429/pic9.png"/>
</center>

b. From the context menu:

<center>
  <img src="/wiki/download/attachments/2523429/pic10.png"/>
</center>

c. From the Options Panel:

<center>
  <img src="/wiki/download/attachments/2523429/pic11.png"/>
</center>

After calculation the tree appears in the MSA Editor in a separate window:

<center>
  <img src="/wiki/download/attachments/2523429/pic12.png"/>
</center>