Aligning sequences with CLUSTAL W

To create an alignment, follow these steps:

  • Import the sequences to be aligned into the Alignment editor.
  • Select CLUSTAL W 1.83 from the Align sequences menu.
  • Choose either the Full alignment or the Quick pair alignment menu items.
  • The alignment progress and status information is displayed while the alignment is performed.
  • At the end of the alignment process, the sequences in the Editor window are now aligned, with dashes indicating inserted gaps.

Shading the alignment:
To provide a visual guide to the alignment, you may color the bases or shade them according to percentage of matched bases in each column (mean-pair score).  To shade the alignment:

  • Select the Color mode menu item from the Options menu.
  • Choose the Color bases or the Mean-score option.

Note:
DNA and protein alignments take place in two steps: an initial pairwise alignment, in which each sequence is compared to each other sequence, and a final multiple sequence alignment.  Choose Full pairwise alignments for greater accuracy, or Quick pairwise alignments for greater speed.