Child pages
  • View, edit and align multiple sequence alignments

Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.
Comment: Migrated to Confluence 5.3

Multiple sequence alignment (MSA Editor). The Alignment Editor is a powerful tool for visualization and editing DNA, RNA or protein multiple sequence alignments. To activate the Alignment Editor open any alignment file. For example you can use the $ugene/data/samples/CLUSTALW/COI.aln file provided with UGENE. After opening the file in UGENE the Alignment Editor window appears:

HTML
<center>
  <br>
  <img src="/wiki/download/attachments/2883700/msa.gif"/>
  <br>
</center>

The editor supports different multiple sequence alignment (MSA) formats, such as ClustalW, MSF and Stockholm. The editor provides interactive visual representation which includes:

  • Navigation through an alignment;
  • Optional coloring schemes (for example Clustal, Jalview like, etc.);
  • Flexible zooming for large alignments;
  • Export publication-ready images of alignment;
  • Several consensus calculation algorithms.

Using the Alignment Editor you can:

  • Perform multiple sequence alignment using integrated MUSCLE and KAlign algorithms;
  • Edit an alignment: delete/copy/paste symbols, sequences and subalignments;
  • Build phylogenetic trees;
  • Generate grid profiles;
  • Build Hidden Markov Model profiles to use with HMM2/HMM3 tools.

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

a. From the toolbar. Click to the tree icon:

HTML
<center>
  <br> 
  <img src="/wiki/download/attachments/2883700/tree_toolbar.gif"/>
  <br>
</center>

b. From the context menu:

HTML
<center>
  <br>
  <img src="/wiki/download/attachments/2883700/tree_context.gif"/>
  <br>
</center>

c. From the Options Panel:

HTML
<center>
  <br>
  <img src="/wiki/download/attachments/2883700/tree_options.gif"/>
  <br>
</center>

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

HTML
<center>
  <br>
  <img src="/wiki/download/attachments/2883700/tree_result.gif"/>
  <br>
</center>