BoxShadeLite Instructions


Step 1.

Open the .aln output file CLUSTALX or CLUSTALW and copy and paste the contents into the text area field on the BoxShadeLite entry form.


Step 2.

Please enter a line number for the reference sequence you would like to use.


Step 3.

Next, select the type of output you would like and click the BoxShade Lite button to display your results.


NOTE:  If running multiple boxshades, you may have to click the refresh button of your browser to display the latest results.  This depends on your browsers cache setting.



Output formats


Pretty Alignment: CLUSTAL alignment viewed as a continuous string as opposed to block format.


Boxshade:  Hightlights Base differences


Hypermutation List:  Parses the alignment file and give the base number and codon of the G to A hypermutation.


G to A Hypermutation Boxshade:  highlights G to A transitions only


                  A to G Hypermutation Boxshade:  highlights A to G transitions only